Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-18 17:57 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 930/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSVA 1.52.3  (landing page)
Robert Castelo
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/GSVA
git_branch: RELEASE_3_19
git_last_commit: f34b397
git_last_commit_date: 2024-06-06 14:14:50 -0400 (Thu, 06 Jun 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for GSVA on nebbiolo1

To the developers/maintainers of the GSVA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GSVA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GSVA
Version: 1.52.3
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GSVA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GSVA_1.52.3.tar.gz
StartedAt: 2024-06-16 23:55:25 -0400 (Sun, 16 Jun 2024)
EndedAt: 2024-06-17 00:06:30 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 665.5 seconds
RetCode: 0
Status:   OK  
CheckDir: GSVA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GSVA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GSVA_1.52.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GSVA.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘GSVA/DESCRIPTION’ ... OK
* this is package ‘GSVA’ version ‘1.52.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GSVA’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
  Running ‘test_gsva_newapi.R’
  Comparing ‘test_gsva_newapi.Rout’ to ‘test_gsva_newapi.Rout.save’ ...16,21c16,21
<     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
<     as.data.frame, basename, cbind, colnames, dirname, do.call,
<     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
<     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
<     pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
<     union, unique, unsplit, which.max, which.min
---
>     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
>     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
>     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
>     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
>     table, tapply, union, unique, unsplit, which.max, which.min
38c38
<     I, expand.grid, unname
---
>     expand.grid, I, unname
161c161
< KEGG_GLYCOLYSIS_GLUCONEOGENESIS                  0.22920126 -0.264187722 -0.37401687  0.291350766  0.17081880 -0.45702585  0.5003620 -0.09626897 -0.47879766  0.2009603094  0.092846463  0.39386860 -0.10064875  0.25767347 -0.006960737 -0.323002689  0.54088138  0.36740468 -0.230653742 -0.21517689 -0.39153412 -0.10416424 -0.0260882429  0.206128783 -0.38394575 -0.26111852  0.11124358 -0.307607156 -0.23108674  0.118623744  0.40568230 -0.35928390 -0.2287986403  0.0674126870 -0.194909729  0.406279736
---
> KEGG_GLYCOLYSIS_GLUCONEOGENESIS                  0.22920126 -0.264187722 -0.37401687  0.291350766  0.17081880 -0.45702585  0.5003620 -0.09626897 -0.47879477  0.2009603094  0.092846463  0.39386860 -0.10064875  0.25767347 -0.006960737 -0.323002689  0.54088138  0.36740468 -0.230653742 -0.21517689 -0.39153412 -0.10416424 -0.0260882429  0.206128783 -0.38394575 -0.26111852  0.11124358 -0.307607156 -0.23108674  0.118623744  0.40568230 -0.35928390 -0.2287986403  0.0674126870 -0.194909729  0.406279736
163c163
< KEGG_PENTOSE_PHOSPHATE_PATHWAY                   0.39571823 -0.352221233 -0.14016244  0.358512977  0.16414025 -0.26589439  0.6674822  0.17953342 -0.55050994  0.0562838685  0.021675321  0.57648156  0.11371008  0.29864451  0.104942610 -0.504014044  0.57693561  0.46862262 -0.257288782 -0.36529987 -0.33598186 -0.39358598  0.1109189257  0.023878095 -0.34214747 -0.25852067  0.28121726 -0.435798801 -0.31480707 -0.007553482  0.26670234 -0.45518879 -0.4532774636  0.2948129840 -0.267281290  0.463433745
---
> KEGG_PENTOSE_PHOSPHATE_PATHWAY                   0.39571823 -0.352221233 -0.14016244  0.358512977  0.16414025 -0.26589439  0.6674822  0.17953342 -0.55049088  0.0562838685  0.021675321  0.57648156  0.11371008  0.29864451  0.104942610 -0.504014044  0.57693561  0.46862262 -0.257288782 -0.36529987 -0.33598186 -0.39358598  0.1109189257  0.023878095 -0.34214747 -0.25852067  0.28121726 -0.435798801 -0.31480707 -0.007553482  0.26670234 -0.45518879 -0.4532774636  0.2948129840 -0.267281290  0.463433745
166c166
< KEGG_GALACTOSE_METABOLISM                        0.06062020 -0.424855520 -0.03930301  0.349652791 -0.12188569 -0.46296074  0.5180153 -0.01789657 -0.35347309  0.2446797481  0.473003017  0.34499007  0.34112213  0.25024239  0.250381767 -0.453215048  0.57769569  0.21561858 -0.337261669 -0.08753488 -0.42331301 -0.04093081 -0.2210103855  0.056226416 -0.07839585  0.07879640  0.27290820 -0.414140702 -0.36050412 -0.191532611  0.39567826 -0.53298775 -0.4127888920  0.3440494486 -0.178365423  0.513262262
---
> KEGG_GALACTOSE_METABOLISM                        0.06062020 -0.424855520 -0.03930301  0.349652791 -0.12188569 -0.46296074  0.5180153 -0.01789657 -0.35356594  0.2446797481  0.473003017  0.34499007  0.34112213  0.25024239  0.250381767 -0.453215048  0.57769569  0.21561858 -0.337261669 -0.08753488 -0.42331301 -0.04093081 -0.2210103855  0.056226416 -0.07839585  0.07879640  0.27290820 -0.414140702 -0.36050412 -0.191532611  0.39567826 -0.53298775 -0.4127888920  0.3440494486 -0.178365423  0.513262262
173c173
< KEGG_PURINE_METABOLISM                           0.20191160 -0.108479208 -0.10596002  0.292297651 -0.05290036 -0.02776887  0.3629813  0.19221693 -0.19257010 -0.1570618328  0.049458419  0.10941378 -0.11575356  0.10624767  0.139611752 -0.104415107  0.24845743  0.18074380  0.044016416 -0.21432408 -0.20002101 -0.17818482 -0.1294276990 -0.149379806 -0.20372875 -0.18695986  0.14562604 -0.027395894  0.03493636  0.032161754 -0.01145234  0.00244119 -0.1717349277  0.1040248755 -0.158512548 -0.016876129
---
> KEGG_PURINE_METABOLISM                           0.20191160 -0.108479208 -0.10596002  0.292297651 -0.05290036 -0.02776887  0.3629813  0.19221693 -0.19257184 -0.1570618328  0.049458419  0.10941378 -0.11575356  0.10624767  0.139611752 -0.104415107  0.24845743  0.18074380  0.044016416 -0.21432408 -0.20002101 -0.17818482 -0.1294276990 -0.149379806 -0.20372875 -0.18695986  0.14562604 -0.027395894  0.03493636  0.032161754 -0.01145234  0.00244119 -0.1717349277  0.1040248755 -0.158512548 -0.016876129
  Running ‘test_plage_newapi.R’
  Comparing ‘test_plage_newapi.Rout’ to ‘test_plage_newapi.Rout.save’ ...16,21c16,21
<     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
<     as.data.frame, basename, cbind, colnames, dirname, do.call,
<     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
<     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
<     pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
<     union, unique, unsplit, which.max, which.min
---
>     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
>     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
>     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
>     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
>     table, tapply, union, unique, unsplit, which.max, which.min
38c38
<     I, expand.grid, unname
---
>     expand.grid, I, unname
  Running ‘test_ssgsea_newapi.R’
  Comparing ‘test_ssgsea_newapi.Rout’ to ‘test_ssgsea_newapi.Rout.save’ ...16,21c16,21
<     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
<     as.data.frame, basename, cbind, colnames, dirname, do.call,
<     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
<     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
<     pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
<     union, unique, unsplit, which.max, which.min
---
>     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
>     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
>     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
>     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
>     table, tapply, union, unique, unsplit, which.max, which.min
38c38
<     I, expand.grid, unname
---
>     expand.grid, I, unname
  Running ‘test_zscore_newapi.R’
  Comparing ‘test_zscore_newapi.Rout’ to ‘test_zscore_newapi.Rout.save’ ...16,21c16,21
<     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
<     as.data.frame, basename, cbind, colnames, dirname, do.call,
<     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
<     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
<     pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
<     union, unique, unsplit, which.max, which.min
---
>     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
>     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
>     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
>     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
>     table, tapply, union, unique, unsplit, which.max, which.min
38c38
<     I, expand.grid, unname
---
>     expand.grid, I, unname
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/GSVA.Rcheck/00check.log’
for details.


Installation output

GSVA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GSVA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘GSVA’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c kernel_estimation.c -o kernel_estimation.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c ks_test.c -o ks_test.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c register_cmethods.c -o register_cmethods.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o GSVA.so kernel_estimation.o ks_test.o register_cmethods.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-GSVA/00new/GSVA/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GSVA)

Tests output

GSVA.Rcheck/tests/runTests.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> oldWarnOptionValue <- options(warn=1)
> BiocGenerics:::testPackage("GSVA")
Timing stopped at: 0 0 0.001
Error in DEACTIVATED("HDF5Array is not yet supported by the new API.") : 
  HDF5Array is not yet supported by the new API.
Running unit tests for input data containers.
Running unit tests for the new API.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
Running unit tests for gsvaParam.
Running unit tests for plageParam.
Running unit tests for ssgseaParam.
Running unit tests for zscoreParam.
Running unit tests for sparse methods.
Please bear in mind that this method first scales the values of the gene expression data. In order to take advantage of the sparse Matrix type, the scaling will only be applied to the non-zero values of the data. This is a provisional solution in order to give support to the dgCMatrix format.
Please bear in mind that this method first scales the values of the gene expression data. In order to take advantage of the sparse Matrix type, the scaling will only be applied to the non-zero values of the data. This is a provisional solution in order to give support to the dgCMatrix format.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
Running unit tests for ssGSEA.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."


RUNIT TEST PROTOCOL -- Mon Jun 17 00:00:20 2024 
*********************************************** 
Number of test functions: 8 
Number of deactivated test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GSVA RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of deactivated test functions: 1 
Number of errors: 0 
Number of failures: 0 
> options(warn=oldWarnOptionValue[["warn"]])
> 
> proc.time()
   user  system elapsed 
 12.474   0.629  13.093 

GSVA.Rcheck/tests/test_gsva_newapi.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> ## 2023-11-10  axel: simple test script for method GSVA, new API
> 
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db


> library(GSVA)
> 
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
> 
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
> 
> p <- 10000 ## number of genes
> n <- 30    ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+             dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
           s1         s2          s3         s4          s5
g1  1.4171739 -1.3444519 -0.99052898  0.4203395  1.30716224
g2 -0.7281951  0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754  0.09779699 -0.6792548 -0.09124045
g4  1.0735382  1.3156255  0.15588330 -1.8079608  0.48531108
g5  0.7229884 -0.9162342  1.93982245  0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+                    paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> gsvaPar <- gsvaParam(X, gs)
> gsva.es <- gsva(gsvaPar, verbose=FALSE)
> dim(gsva.es)
[1] 100  30
> gsva.es[seq.int(min(nRowsToPrint, nrow(gsva.es))),]
               s1          s2           s3          s4          s5            s6           s7           s8           s9          s10          s11          s12         s13          s14          s15          s16          s17          s18          s19         s20          s21          s22         s23          s24         s25           s26           s27          s28          s29         s30
gs1  -0.108156444  0.16592613 -0.143808928  0.11391879 -0.08600850 -0.1734242744  0.178707342  0.017723667  0.094198786  0.103231011  0.098990086  0.056687452 -0.19582109  0.012296862  0.162223446 -0.114766326 -0.293330673  0.126367035  0.228829622 -0.14884956  0.026620947 -0.301784054 -0.30631599  0.235331985  0.04638816 -0.1100099596 -0.0999704513 -0.046424755  0.293447378 -0.17344608
gs2  -0.078540545  0.19300391  0.079182716  0.07049058  0.04007773  0.1715072044  0.203277577 -0.081465590  0.233451158 -0.280324459  0.037382517  0.025061259  0.10845168 -0.059159170  0.026844586 -0.179610527 -0.014413382 -0.006820970  0.160768137 -0.03932893 -0.108749046 -0.282019527  0.08605189  0.088382420  0.06394081  0.0207049280  0.2183498851  0.084518747 -0.272555793 -0.17000646
gs3  -0.012507633 -0.25351738  0.102368361  0.03512929 -0.04994980  0.2133058738  0.039178136  0.191682501 -0.398094428  0.343111543 -0.076791958  0.119069468  0.20772960 -0.421116272  0.459538877 -0.026465562  0.049041138  0.038384015 -0.227781747 -0.09134458 -0.514150386  0.102494298 -0.20024782  0.058491931  0.31836609  0.0290482835 -0.1935787866  0.254416177 -0.017322981  0.13715416
gs4  -0.083248846  0.02946102 -0.042556750  0.08145113 -0.05401867  0.1055847509 -0.158661388  0.009278808 -0.107756958 -0.016141791 -0.033233344  0.016122676 -0.08342913 -0.003621483  0.141048462 -0.001454018  0.129386313 -0.062100704 -0.110927318 -0.16530100 -0.059697155  0.032076675  0.03158162  0.038234047 -0.03942766  0.0886365597 -0.0782910850  0.014516781 -0.046885905  0.20075530
gs5   0.129917233 -0.14323749 -0.172890947  0.13411529  0.09628743  0.0265475253  0.050870369  0.174122516  0.081836827 -0.011085820  0.023089550  0.056006287 -0.07140253  0.055193034 -0.091548680 -0.149492965  0.037312222  0.002985924 -0.144101863 -0.01888358 -0.065961297 -0.132468115 -0.06377434  0.028402402 -0.07610908  0.0853809151  0.0806035221 -0.015568714 -0.047153650  0.01778386
gs6  -0.284972014  0.13823428 -0.210772112 -0.05757943  0.10388699  0.1439391564  0.109157571  0.077447106  0.001144118  0.181326976 -0.019716350 -0.006386486 -0.06006467 -0.189315716  0.005405993 -0.001953525  0.006055122  0.159361735 -0.089341440  0.02743543  0.000728224 -0.178928406  0.19578172 -0.036394549 -0.07703071  0.0784321711 -0.0863070990 -0.033617568 -0.088131880  0.09008523
gs7   0.028701964  0.23235456  0.119915418 -0.01970966 -0.13698294  0.0031401764 -0.218020511 -0.195273449  0.038952752 -0.232984107  0.037413398  0.092363954  0.18259907  0.053162383  0.097674825 -0.128073348  0.073567722  0.115641271  0.030537867 -0.13049139 -0.057022525  0.056026838  0.06828574 -0.001000666 -0.06071745  0.0039744122 -0.0005585096 -0.009440488  0.080790372 -0.09940113
gs8   0.006333045  0.01460128  0.136198133 -0.07889863 -0.11123825  0.0387444491 -0.002037746  0.040187847 -0.121686486 -0.095484760  0.052264970  0.150236692  0.04926308 -0.109888308  0.100412242  0.146400621 -0.156050604  0.018922498  0.067657595 -0.05343596 -0.068927042 -0.080941576  0.07501949  0.007660285  0.16079137 -0.2682601362  0.1012140737  0.042776107  0.002111495 -0.05482992
gs9  -0.175865699 -0.19690763  0.060751759  0.18933359 -0.25345038 -0.5016097134 -0.138854281 -0.543295516 -0.263543869  0.275493131  0.127068488 -0.189846149 -0.25784051 -0.094258279  0.079039460 -0.165487585  0.343543465  0.357424759  0.292115383 -0.02178526  0.058171774 -0.034552813  0.23880691  0.043569142 -0.02980941  0.2945856247 -0.0219706361 -0.176772536  0.532204432  0.15142975
gs10  0.098112170 -0.35611542 -0.056579211 -0.21958226  0.08809195  0.0009137342  0.405507850 -0.115481827 -0.187608357  0.275280555 -0.119567715  0.109071314 -0.25466878  0.000375529  0.367963754  0.188641874 -0.079209335  0.256239935 -0.125622141 -0.11854834  0.255106701  0.471876454 -0.37385722  0.223837887  0.02289076 -0.4287911223  0.0067681070 -0.240476346  0.088671730 -0.17764056
gs11  0.098198198  0.25911849 -0.038035464 -0.21771367  0.50403680  0.4428564710  0.303629955  0.175137764  0.098749107  0.336354436  0.130586418 -0.052651015 -0.20599477 -0.223219535 -0.250927738 -0.509205728 -0.444857809 -0.045479124  0.088547534 -0.02722749 -0.099107700 -0.092392768  0.05594057 -0.069222681 -0.02071750 -0.5973180441 -0.1580304020  0.577149382  0.298070860 -0.07458713
gs12  0.096490065 -0.02605933 -0.022030360 -0.13719093  0.02682772  0.0434813048 -0.028867424  0.014475285  0.133723333  0.034558185  0.137695531 -0.258037193 -0.02835015 -0.064346101 -0.026710216 -0.269826308  0.021532017 -0.047943462 -0.022440279  0.16687604  0.055835937  0.023685654 -0.06486901 -0.020025683  0.02178566  0.0480895384  0.1113867112  0.059878337 -0.055779061  0.06729589
gs13  0.223982459  0.20679601  0.258716670 -0.20136940 -0.20071529  0.2464442479  0.258963232 -0.110149641 -0.089442650  0.205739275 -0.165291846 -0.150888458 -0.15226578 -0.404364664 -0.005312768 -0.100572023 -0.220803462 -0.043370760  0.309185329 -0.08715961  0.326811093  0.080713114 -0.10705436  0.116977351  0.19046277 -0.1469583728  0.1367810954 -0.242162288 -0.021163531 -0.29632096
gs14  0.024001674 -0.26723135 -0.398236422  0.24294428  0.04991522 -0.1433770344  0.399168882 -0.248011836 -0.121856855 -0.141859978 -0.080548602  0.105372091  0.28663719  0.303516623  0.320574969 -0.044182057 -0.177554197 -0.058580934  0.063071784  0.11623764  0.096538164 -0.055513833 -0.42073250  0.001550673  0.16488985  0.0464015474 -0.0156188987 -0.085775207 -0.160086709  0.12477191
gs15  0.107236756  0.02674424  0.186569862 -0.12214378 -0.06518532 -0.0612943018 -0.111903203  0.049803938  0.044035633 -0.049752082 -0.024069020  0.205529366 -0.10569735  0.002119758 -0.140742436  0.185481189 -0.005853900 -0.101479169 -0.001425559  0.08308067  0.020882554  0.051697561  0.05197634  0.276490515  0.09494653 -0.1604533503 -0.1106884939 -0.115292890 -0.212477678 -0.04261664
gs16 -0.189661090  0.18212481 -0.194291062  0.11967900 -0.10434220 -0.1191397416  0.039057392 -0.039343595 -0.060222683 -0.067506938 -0.160259179  0.001722109  0.14378774 -0.013559159  0.165627072 -0.022929924 -0.032725397 -0.021268004 -0.036164578  0.04105859  0.054069320 -0.023626997  0.01312951 -0.066479935  0.03594310  0.0510113983  0.0168947880 -0.006306806  0.182001699  0.08182702
gs17 -0.224154710 -0.06839924  0.011942989  0.06596303 -0.01898285 -0.0787236017  0.262432764  0.128350415  0.107171841 -0.036418415  0.004430908 -0.152391953  0.13910575 -0.034949755  0.129033846 -0.096575805  0.027781998  0.086966986 -0.057041784  0.06413185 -0.088718911  0.119981085  0.07640730 -0.116205119 -0.19211361  0.0949234199 -0.0301489984  0.007364308 -0.021454055 -0.05405507
gs18  0.144462699  0.15190319 -0.005644637  0.13442504 -0.06851005 -0.0650767309  0.132965207 -0.072143414  0.065609258 -0.169604968  0.149226527 -0.127080390  0.15127334  0.001524110 -0.096672404  0.138052662  0.156721335 -0.113260460 -0.055010361 -0.11281271 -0.081498926 -0.062627336  0.01138976  0.083051492 -0.11650835 -0.0644334115  0.0158668194 -0.035534584 -0.216520795  0.25451909
gs19 -0.114727405  0.11606640  0.014639537 -0.04539144 -0.15632885 -0.3008348682 -0.045227873  0.057911106  0.077993588  0.122127072  0.004180167 -0.010181304 -0.13058749 -0.017522472 -0.063018173  0.096067773  0.059813582 -0.042255247 -0.110140982  0.28341206 -0.057751403 -0.062970017 -0.26428505 -0.087882907 -0.06031966  0.2005231419  0.0555096129 -0.119697294  0.158883568  0.13631818
gs20 -0.250434807 -0.04667705  0.049213711  0.05304980  0.15123353  0.1091531262  0.061807069 -0.184158384  0.116516282 -0.024996495  0.050439116  0.062684587 -0.03915131 -0.056457080 -0.298840942  0.163262104 -0.029174994  0.169067340  0.055693074  0.03338657  0.068733916  0.047318574  0.05085801  0.007052938 -0.13510237 -0.0802436967 -0.0251620082 -0.048587104 -0.071021904 -0.04269538
gs21  0.135378868  0.16802591 -0.029364914 -0.05595578  0.06148837  0.0971278669  0.093694989 -0.069804459  0.025767351 -0.016170741 -0.101534883 -0.120160395  0.04062725  0.048721679  0.095192931 -0.186471874 -0.048112890 -0.212895052 -0.006971640 -0.06755367 -0.127602218 -0.002382844 -0.01605748 -0.001335954 -0.11991648  0.2219113569  0.1352495887  0.023381243  0.045687474  0.09964681
gs22 -0.163680317  0.18690317 -0.148456673 -0.05079516  0.24365056 -0.0822628950  0.098769260 -0.142649660 -0.444454723  0.065727715  0.247342235 -0.167215276  0.14197399  0.112681184 -0.092957822 -0.152497158 -0.190680030  0.035186284 -0.035122161  0.07290296  0.002562072  0.032535170  0.26649228  0.318514935 -0.22440917 -0.0178361034 -0.3138866671  0.416817320 -0.314242601 -0.02772554
gs23  0.018766631  0.11521514 -0.014809625  0.06153311  0.12707575  0.1281180662 -0.064456890 -0.030536563 -0.129612935 -0.015034995  0.129955588  0.057111134 -0.22165829  0.160845001  0.108799691  0.090243195  0.008299278  0.041996865  0.155112600 -0.08959788  0.079998925  0.013571384 -0.27985106 -0.134362071  0.05587958  0.0900157601 -0.0306708210 -0.124824057 -0.125258066  0.03409850
gs24  0.389869244  0.28790219 -0.049088266 -0.14811747 -0.19067680 -0.3358219719 -0.236811755  0.135616593 -0.238985451  0.206904619  0.248194834 -0.112405472  0.09072771 -0.142415602 -0.383217061  0.363554498  0.187395921 -0.327457108 -0.592050113  0.15802933  0.479729800 -0.150610477  0.28243874 -0.202986917  0.12126635  0.0007700638 -0.0280707676  0.049077412 -0.212219932  0.12363971
gs25  0.093907002 -0.08177613  0.137542184  0.01817976 -0.07335024 -0.2779884851 -0.010150488 -0.109990320 -0.023037802 -0.006390004  0.088013029 -0.003651291 -0.16541049  0.090206786 -0.091065047  0.089689390  0.061729248  0.223324387  0.050045901 -0.08299866  0.221155832 -0.246784249  0.32074709  0.037550027 -0.16709326 -0.1213934826  0.1061837744  0.016007278  0.065201658 -0.19524119
> 
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+                     featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+                     sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+                                       grep("^REACTOME", names(c2BroadSets)),
+                                       grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- gsvaParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+                       minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
                                                    NA19099       NA18523      NA19144     NA19137      NA18861     NA19116     NA19130     NA19131      NA19119     NA19152       NA19153     NA19140      NA19138     NA18522      NA19192     NA19193     NA19239      NA19238      NA19210      NA19201     NA19172      NA18870     NA18858     NA18852     NA19159      NA18855     NA19204      NA18501     NA19127      NA19098      NA19093      NA18856       NA18912     NA18517      NA18502      NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                 -0.14418012 -3.133817e-01 -0.391171673  0.21340339  0.398980386 -0.03179434  0.17524757  0.26705934  0.196519789  0.07076882  0.0145998761  0.27413667  0.083361420 -0.10575923 -0.189608055 -0.30624818 -0.25363521 -0.371666584  0.131382543  0.122449569  0.19101441 -0.452577261 -0.23105310  0.10274129  0.13624827 -0.007124138  0.15976388 -0.102152201 -0.19832123  0.202573385  0.378578854  0.288352608  0.0016120367 -0.36268281  0.110141001  0.255205365
KEGG_CITRATE_CYCLE_TCA_CYCLE                    -0.20263269  2.546732e-01  0.012685194 -0.23423639  0.166963123 -0.19060735 -0.09504444  0.02350579  0.252153864 -0.29870033  0.3426900775  0.11865360  0.158070942  0.43950013 -0.113554675 -0.41027161 -0.51496205  0.101464045  0.023147027  0.213518494 -0.29129288 -0.365361233  0.19537441  0.34046332 -0.29053602 -0.136804277 -0.03945536 -0.046177552 -0.15861718 -0.197363503  0.005305269  0.139063426  0.3753961988 -0.11672606  0.399275124  0.081808177
KEGG_PENTOSE_PHOSPHATE_PATHWAY                   0.13384996 -3.426199e-01  0.011055653  0.10473591  0.533196442  0.08319882 -0.07286230  0.33986046  0.183712674 -0.02112598  0.3436817431  0.14970027  0.045619795  0.34106103 -0.319187004 -0.12337277 -0.52047602 -0.079296210  0.246091695  0.007442165  0.29667112 -0.493628865 -0.37567090  0.04398852 -0.10380781 -0.066433829  0.07248245 -0.134640505 -0.28388477 -0.007933863 -0.010660832  0.409249866 -0.0593083889 -0.20730184  0.135344012  0.328985231
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS   -0.04814412  2.649390e-01 -0.247781616 -0.57051071 -0.151893395 -0.12257602 -0.22484133  0.15415444  0.170044654 -0.41770107  0.4059486427  0.32600904 -0.337637004  0.45224654  0.240860923 -0.52860069  0.06878373  0.238734193  0.199127444  0.197382585  0.19194776 -0.280713555 -0.14573199 -0.07489534 -0.17115751 -0.356340540  0.19199016  0.464332824 -0.30954147  0.066784875  0.107764195 -0.244087607 -0.0038072528 -0.15577831  0.159465388  0.173314410
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM            -0.05277464 -2.559473e-01 -0.272606595  0.02654463  0.466256330 -0.07516578 -0.08827428  0.17940166  0.175438074  0.08335115  0.1949276528  0.03263319 -0.037187373  0.21769233 -0.056026638 -0.21875825 -0.41789351 -0.167172773 -0.116119580  0.028778964  0.18475990 -0.006106045 -0.35983263  0.04835565  0.13058334  0.320582420  0.14792337 -0.356458053 -0.32573808 -0.200330955  0.256816456  0.243425591  0.1799096212  0.04042810  0.078246331  0.111827102
KEGG_GALACTOSE_METABOLISM                       -0.51060398 -3.263793e-01 -0.339445527  0.18058711  0.590147665 -0.05433206 -0.02631533  0.01150479  0.112418121  0.20086931  0.0758757516  0.18135031  0.172899748  0.09960453 -0.419887121 -0.30998273 -0.41031657 -0.552555465  0.134889700  0.312990925  0.40442648 -0.314101297 -0.45866474  0.24674708  0.36744079 -0.300764693  0.46807677 -0.119986976 -0.47812839 -0.137744193  0.179487063  0.362685887 -0.1178698280 -0.27717714  0.333123866  0.570589012
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM           0.39533716  1.058190e-01 -0.055948980  0.32042238  0.117469296 -0.47857258 -0.27397801  0.48975038 -0.092440191 -0.05795173 -0.0744286061 -0.21729660  0.193086799  0.31390769  0.038143586  0.04976352  0.06941386 -0.243260211 -0.075892533 -0.136936205 -0.70456483 -0.248431863  0.04441643  0.16407617  0.10523266  0.201548537 -0.63041976 -0.064796304 -0.42586995  0.071454531  0.327254119 -0.007811551  0.2006101479  0.02592733 -0.340917460  0.307433176
KEGG_FATTY_ACID_METABOLISM                       0.03299573  1.864144e-01  0.209909423 -0.24436698  0.207945636 -0.12244431 -0.23816823  0.49912101  0.388462885 -0.20945911  0.0991996326  0.28644900  0.027816218  0.13251193 -0.076840810 -0.35401475 -0.26281629  0.022061212  0.092216454  0.131207009 -0.32302048 -0.043107375 -0.17671170  0.13894499 -0.29064351 -0.119433589 -0.42265454 -0.103764267 -0.09629923 -0.114672086  0.246246155  0.137119878  0.4886075270 -0.07587824  0.017144468  0.033774833
KEGG_STEROID_BIOSYNTHESIS                        0.19815359 -1.774636e-01 -0.495105675 -0.25914877  0.190294265 -0.32446562  0.40274807  0.55575502  0.334577780 -0.30738356  0.0995344990  0.02714295 -0.341505856  0.33481474  0.483575947 -0.46782536 -0.41070981  0.363247663 -0.316476327  0.186672062  0.06775463 -0.460614122 -0.03811347  0.10403630  0.19161113 -0.276517655 -0.31751788 -0.335291201  0.04610323  0.498441393  0.203641470  0.258537460  0.1025848927  0.32986280  0.106728771  0.044375942
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS             -0.22772338  3.313823e-01 -0.045122587  0.34604215 -0.326387527 -0.37238068  0.38109784  0.50612839 -0.279733901 -0.46710624 -0.3566433892  0.38150788 -0.160181485  0.32343792 -0.389633800 -0.04093348 -0.34781666  0.439898619 -0.553153746  0.333311581 -0.41569720  0.089984351  0.11640121  0.49616048 -0.18515617 -0.288891006 -0.25307258  0.488505183  0.48932043  0.685621131  0.405112800 -0.410676806  0.0705999647  0.46798357 -0.050407919 -0.059580749
KEGG_STEROID_HORMONE_BIOSYNTHESIS                0.36585090 -4.158145e-02 -0.314872488  0.36177011 -0.117186424 -0.57565233  0.06555161  0.12421684 -0.154537531 -0.03651661  0.2548932547 -0.25983105 -0.191491808 -0.01727654  0.007925232  0.20173611  0.07385251 -0.151691776 -0.174246389  0.170112989 -0.31138189 -0.287770962 -0.32224067  0.25539717  0.10328113 -0.240352841 -0.02844086  0.115892938  0.20532852  0.092026010  0.444749927  0.138675375 -0.1017217201  0.19796954 -0.321674802  0.386149959
KEGG_OXIDATIVE_PHOSPHORYLATION                  -0.44614351  4.066706e-01  0.315683836 -0.38414333 -0.062919018  0.19858654 -0.22582769  0.04161922 -0.079644512 -0.05102341  0.3664592628 -0.09619084  0.197886790  0.31353680 -0.184933831 -0.36350759 -0.30233809  0.313796606  0.236200087 -0.322015323 -0.29790565 -0.196993574 -0.08707882  0.26462100 -0.24626717  0.241984062  0.12731683 -0.209160519 -0.13913537 -0.164019798  0.003657569  0.174518566  0.2846868562 -0.03739754  0.351418754 -0.151465743
KEGG_PURINE_METABOLISM                          -0.12658061  6.074446e-05  0.109942629  0.02507931  0.152633778  0.20438698  0.05049747  0.08805693 -0.163334045 -0.09018816  0.2671088095  0.13157027  0.002135794  0.19941825 -0.014318164 -0.19467600 -0.19570945  0.160038352 -0.003976608 -0.159354533  0.04953516 -0.237144513 -0.19729598  0.06518253 -0.20013531  0.065168510 -0.02813078  0.001056042 -0.03466977 -0.006764599  0.054072961 -0.010634495  0.1220901659 -0.14216130  0.002592869 -0.079175937
KEGG_PYRIMIDINE_METABOLISM                      -0.08169375  2.124920e-02  0.237112503  0.02740654 -0.007840300  0.24898451 -0.04095103  0.23335111 -0.156235016 -0.16193850  0.2906078400  0.19091514 -0.095748971  0.19881417  0.039922114 -0.17823010 -0.14678724  0.256232748  0.020947130 -0.088582706  0.16161796 -0.307232427 -0.08240158  0.03008501 -0.30460678  0.090542640 -0.09034804 -0.174657514 -0.09426947 -0.129635921 -0.040660453 -0.066351934  0.3336055751 -0.05856322 -0.032156131 -0.179871004
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM -0.13254287 -6.225182e-02 -0.134319540 -0.15729012  0.026834849 -0.22343907  0.14168564  0.30713913 -0.125172326 -0.17862058 -0.1731094263  0.30055821 -0.085420317  0.09882301  0.193697084  0.31425985 -0.31600195 -0.125372528  0.295397875  0.180199556 -0.20500280  0.058617241 -0.14777995  0.05091438  0.12367397 -0.040310943 -0.08013473  0.182346297 -0.10198293  0.197362551  0.285434513  0.083269169 -0.3708006909 -0.06111266 -0.243366412  0.222746237
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM     0.10719371 -4.606961e-01 -0.180567057  0.09540174  0.245012608 -0.15656927  0.22420420  0.05451998  0.279637623  0.13353399  0.0588075025 -0.29202943 -0.043946876  0.01212064  0.153895823  0.41802493 -0.13778592 -0.372235469 -0.406109789  0.283133835  0.19519783 -0.020078578 -0.26407215  0.12285472  0.26704639  0.059250879  0.04897781 -0.250007490 -0.05255973  0.087369877  0.196707759  0.202125900 -0.4079062250 -0.14271079  0.201471466  0.148775715
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM          0.31199860 -1.470030e-01  0.003351767  0.19314634 -0.069733318  0.03818098  0.14330053  0.29773728  0.199561609 -0.18575435  0.2414974155  0.26605667 -0.291208656  0.16923947  0.350632975  0.15181300 -0.22743772 -0.019995533  0.165918443 -0.282999158  0.23210130 -0.390498560  0.09366624 -0.22502795 -0.10851096 -0.372625112 -0.43938185  0.172251073  0.03236597  0.169871903 -0.116676657 -0.006200565 -0.2279015972 -0.18233790  0.215082562 -0.127529151
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION   0.13690035  3.114732e-01  0.066312869 -0.42482813 -0.090282754  0.17692622 -0.19729696  0.34694241  0.407012719 -0.49732087  0.4128185814  0.21841977  0.209032500  0.22079194  0.098804076 -0.28545919 -0.23815839 -0.180999045  0.227212036  0.266627679 -0.26343085 -0.365422361 -0.24682867  0.09025547 -0.26797947 -0.355998344 -0.48059599  0.287997010  0.04787260  0.218397773  0.054137782 -0.098018435  0.3267593437 -0.45818263  0.271972064  0.296388858
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS  0.21018404  3.311632e-01 -0.305891231 -0.40884425  0.154601400  0.29113672 -0.24105148 -0.24181442  0.181954325 -0.58092775  0.4049453421  0.24614645  0.133009367  0.50265059  0.272676320  0.03717033 -0.02236702 -0.145501442  0.138011286  0.443984308  0.39650468 -0.290692301 -0.12632929 -0.19057616 -0.07228556 -0.257796347  0.05090257 -0.239289854 -0.27079693 -0.411150458  0.112237525 -0.264314957 -0.4438365768  0.26411102  0.709862664 -0.016572984
KEGG_LYSINE_DEGRADATION                         -0.05052662  1.114498e-02  0.229382702  0.09046133  0.038741982  0.28814839 -0.18110222  0.18668860  0.200429660 -0.15730855  0.2122002799  0.15678305  0.291243079 -0.09136060  0.075543036 -0.20498916 -0.11109630 -0.119030450 -0.042852292  0.236306523  0.07759842 -0.290175631 -0.01746742 -0.21890493 -0.20792480  0.077495323 -0.27615714  0.039431840 -0.12276895 -0.053898732 -0.080541817 -0.016639943  0.0009973473 -0.40134082  0.137262457  0.007682097
KEGG_ARGININE_AND_PROLINE_METABOLISM            -0.22800596  4.906206e-02 -0.042335265  0.01804139  0.185198410 -0.31622084  0.33887630  0.14716659 -0.125964421 -0.04372424 -0.1317531626 -0.23684263 -0.084937438  0.12230128  0.041463950  0.01888723 -0.23867163 -0.418034734  0.100108084 -0.024241225  0.06662724  0.062701077 -0.18005295  0.28126338  0.26487393  0.117918976  0.03282485 -0.267823209 -0.11043893  0.310700224  0.208244241  0.293517379 -0.1408712737  0.08681285  0.022305834  0.089895339
KEGG_HISTIDINE_METABOLISM                        0.36390137  2.365551e-01 -0.116603139 -0.05003836  0.327736448 -0.21045969 -0.09444006  0.07411204  0.004241093 -0.21347825 -0.2759296517 -0.09004815 -0.220892221 -0.04865282  0.223799615  0.07800378  0.10695352  0.008719129 -0.157708191 -0.206105926 -0.07079359  0.329843813 -0.03292310 -0.12534816  0.15073847 -0.369373567 -0.44170643  0.302626017 -0.35207965  0.319661614  0.084963193 -0.328337412  0.0562137944 -0.01801214 -0.140975452 -0.224081075
KEGG_TYROSINE_METABOLISM                         0.20007757  1.721769e-01 -0.037643348 -0.19625928 -0.075882501 -0.12591313  0.33248542 -0.07760137 -0.191628836 -0.18678014  0.0004931861 -0.41470470 -0.197618861  0.44585904  0.460970463 -0.23734373  0.06323644  0.447147523 -0.339999748 -0.263094997  0.32393110  0.148291697 -0.02476993 -0.16845439 -0.05628810 -0.228433500 -0.09241908  0.205241359 -0.14005676 -0.123163041  0.280135889 -0.404510468 -0.0076082103  0.41987347  0.046111365 -0.109788331
KEGG_PHENYLALANINE_METABOLISM                    0.14876060  3.091885e-01 -0.425309307  0.03290077  0.007314721 -0.44139027  0.41683218  0.00264260 -0.665142859  0.33683691 -0.1354678721 -0.56429899 -0.339302707  0.23461582  0.388641234 -0.14178018 -0.13963600  0.402700359 -0.060552296  0.198533242  0.30608114 -0.367173008  0.39977893  0.09861950  0.19457836 -0.450408082  0.02414787  0.419408775  0.14007478 -0.167643347  0.038509810 -0.118899152 -0.4538199574  0.58568820  0.155660090 -0.409252364
KEGG_TRYPTOPHAN_METABOLISM                       0.02771378  7.276144e-02  0.164993365 -0.04842795  0.275480475 -0.39691784 -0.07428901  0.25507776  0.187930224 -0.16961352 -0.0772668699  0.10285172 -0.067196121  0.10898541 -0.204308026 -0.07494849 -0.14783141 -0.200577850  0.338704351  0.030157577 -0.38063449 -0.187786425  0.04954516 -0.07650680  0.08969431 -0.024503220 -0.28162674  0.105474846 -0.15358250 -0.063342825  0.059069680 -0.027357901  0.4168932938  0.08101763 -0.197098915  0.014085911
> pickrellPar <- gsvaParam(pickrellCountsArgonneCQNcommon_eset,
+                          canonicalC2BroadSets, minSize=5, maxSize=500,
+                          kcdf="Poisson")
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esrnaseq)[seq.int(min(nRowsToPrint, nrow(esrnaseq))),]
                                                    NA19099      NA18523     NA19144      NA19137     NA18861     NA19116    NA19130     NA19131     NA19119       NA19152      NA19153     NA19140     NA19138     NA18522      NA19192      NA19193     NA19239     NA19238      NA19210     NA19201     NA19172     NA18870       NA18858      NA18852     NA19159     NA18855     NA19204      NA18501     NA19127      NA19098     NA19093     NA18856       NA18912       NA18517      NA18502      NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                  0.22920126 -0.264187722 -0.37401687  0.291350766  0.17081880 -0.45702585  0.5003620 -0.09626897 -0.47879766  0.2009603094  0.092846463  0.39386860 -0.10064875  0.25767347 -0.006960737 -0.323002689  0.54088138  0.36740468 -0.230653742 -0.21517689 -0.39153412 -0.10416424 -0.0260882429  0.206128783 -0.38394575 -0.26111852  0.11124358 -0.307607156 -0.23108674  0.118623744  0.40568230 -0.35928390 -0.2287986403  0.0674126870 -0.194909729  0.406279736
KEGG_CITRATE_CYCLE_TCA_CYCLE                     0.19534471 -0.202157014 -0.31886736  0.257353003  0.09452472 -0.14337654  0.5803541  0.21971004 -0.48460389 -0.0910376333  0.143073239 -0.01343428  0.21924711  0.14911562  0.331156020 -0.623445470  0.26517213  0.10217269 -0.244826732 -0.08275136 -0.13342326 -0.18991201  0.2222643203 -0.008264954 -0.27726336 -0.32626055  0.55391119 -0.274223459 -0.41600613 -0.239476881  0.23644605 -0.33329094 -0.4140553740  0.3505474463 -0.034676768 -0.002314262
KEGG_PENTOSE_PHOSPHATE_PATHWAY                   0.39571823 -0.352221233 -0.14016244  0.358512977  0.16414025 -0.26589439  0.6674822  0.17953342 -0.55050994  0.0562838685  0.021675321  0.57648156  0.11371008  0.29864451  0.104942610 -0.504014044  0.57693561  0.46862262 -0.257288782 -0.36529987 -0.33598186 -0.39358598  0.1109189257  0.023878095 -0.34214747 -0.25852067  0.28121726 -0.435798801 -0.31480707 -0.007553482  0.26670234 -0.45518879 -0.4532774636  0.2948129840 -0.267281290  0.463433745
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS    0.30431379 -0.234295884 -0.27059673 -0.245346011 -0.06027442  0.04706860  0.3884300 -0.15945758  0.02075130 -0.0008356316  0.156613047 -0.06726357 -0.25892817  0.47051857  0.358948273 -0.512413738  0.41386623  0.25956799  0.146563139 -0.10384415  0.29375249 -0.32605966 -0.3406774353 -0.079363956 -0.25850079 -0.55407022  0.33385389  0.468934430 -0.03022371  0.104853773  0.29678304 -0.14204144  0.3091341703 -0.0449204187 -0.269151573  0.118249851
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM             0.11231761 -0.062748045 -0.04494400  0.443120939 -0.43879510 -0.26298245  0.4742617  0.10248633 -0.35537405  0.1685276920  0.144103617  0.21438430  0.15584943  0.01726953  0.220675430 -0.319381715  0.48892920  0.46105569 -0.426727337 -0.19856115 -0.31952483  0.01320194 -0.0382402740 -0.043511121 -0.35219578 -0.12906627  0.26969235 -0.290367845 -0.32181822 -0.242589300  0.35793456 -0.18587339 -0.3767879009  0.3985766414 -0.191002663  0.343416703
KEGG_GALACTOSE_METABOLISM                        0.06062020 -0.424855520 -0.03930301  0.349652791 -0.12188569 -0.46296074  0.5180153 -0.01789657 -0.35347309  0.2446797481  0.473003017  0.34499007  0.34112213  0.25024239  0.250381767 -0.453215048  0.57769569  0.21561858 -0.337261669 -0.08753488 -0.42331301 -0.04093081 -0.2210103855  0.056226416 -0.07839585  0.07879640  0.27290820 -0.414140702 -0.36050412 -0.191532611  0.39567826 -0.53298775 -0.4127888920  0.3440494486 -0.178365423  0.513262262
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM           0.51820705  0.039968658 -0.12377878 -0.036122904  0.31985771 -0.46527398  0.3988617  0.01038232  0.37687330  0.5270758669 -0.001642410 -0.11679805 -0.05628187  0.71772103  0.241534280 -0.289882381  0.69553991  0.45968207  0.296411226 -0.50738472 -0.41554732 -0.27269571 -0.0503383811  0.414487589 -0.23400690 -0.52790283 -0.51602401  0.445718811 -0.42330633  0.174908837 -0.07311759  0.34397307  0.2085765041 -0.3221300091 -0.392502279  0.284751348
KEGG_FATTY_ACID_METABOLISM                       0.20886138 -0.242876900 -0.30320811  0.187550569  0.29327773 -0.08700294  0.5230685  0.27380231 -0.34116554  0.1472345229  0.062594388  0.08687790  0.14291551  0.51283780  0.291434806 -0.504476008  0.43294161  0.28219716 -0.304791635 -0.30535668 -0.18442492 -0.13244662  0.0150691534  0.283488006 -0.48289609 -0.49976986  0.09652311 -0.011347711 -0.31278105  0.239631877  0.20679322 -0.03829960 -0.3295649579 -0.0001742616 -0.141024787  0.339491609
KEGG_STEROID_BIOSYNTHESIS                        0.33604553  0.078851347 -0.52590310 -0.263728541  0.32226372  0.07485904  0.3016156  0.28921483 -0.28561530 -0.6241643849 -0.150031690 -0.31567564  0.10600143  0.12621865  0.040239055 -0.372783352 -0.17192551 -0.02763554 -0.362917924 -0.33311374 -0.30449600 -0.19719698  0.6253409182 -0.008988029  0.19293398  0.09900056  0.13681999 -0.119518167 -0.26419274 -0.013995204  0.20395478  0.11325134  0.1626070916  0.5348477961  0.511074525 -0.190211341
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS              0.15739882  0.084600205 -0.52857163  0.553659439  0.26308379 -0.59676812  0.1225233  0.47452481  0.39641389 -0.4648496916 -0.432446416  0.25929223  0.48938377 -0.03614696 -0.087619025 -0.409483402 -0.39069390  0.44383724 -0.217291058 -0.06841149 -0.20808586  0.30133475  0.2338089031  0.628743013 -0.21619683 -0.24904089 -0.29348796  0.201532148  0.37954912  0.371373220  0.35506241  0.16613077 -0.1045489108 -0.3541049382 -0.187847376  0.005129543
KEGG_STEROID_HORMONE_BIOSYNTHESIS                0.38438742  0.113162544 -0.45530979  0.357007701 -0.25621878 -0.29318119 -0.1569740  0.14898979  0.39668852 -0.0468902937 -0.117557120 -0.02018489  0.05524139  0.23740098 -0.066581664  0.258410115  0.10847272 -0.13068365 -0.211051369 -0.28866137 -0.15360410  0.38750091 -0.3238802927  0.274917265  0.25281933  0.01163520 -0.01972985  0.521392285  0.25890358 -0.202780567  0.14930619  0.49695425 -0.0003891365 -0.4015589637 -0.319750989  0.216079876
KEGG_OXIDATIVE_PHOSPHORYLATION                   0.03439798 -0.068230945 -0.24335287  0.179558503 -0.07748180  0.23899287  0.5355567  0.10928544 -0.58653812 -0.1232948723  0.011594465  0.25516015  0.10959538  0.23121819  0.196992997 -0.214021354  0.13140917  0.22589733 -0.167995266 -0.12327534  0.02643072 -0.11175039  0.0487111545 -0.293168402 -0.43460403 -0.36521148  0.06558919 -0.309035960  0.24113723 -0.186432466  0.25366326 -0.01546476 -0.1003451715  0.2488324612 -0.323304803 -0.197206582
KEGG_PURINE_METABOLISM                           0.20191160 -0.108479208 -0.10596002  0.292297651 -0.05290036 -0.02776887  0.3629813  0.19221693 -0.19257010 -0.1570618328  0.049458419  0.10941378 -0.11575356  0.10624767  0.139611752 -0.104415107  0.24845743  0.18074380  0.044016416 -0.21432408 -0.20002101 -0.17818482 -0.1294276990 -0.149379806 -0.20372875 -0.18695986  0.14562604 -0.027395894  0.03493636  0.032161754 -0.01145234  0.00244119 -0.1717349277  0.1040248755 -0.158512548 -0.016876129
KEGG_PYRIMIDINE_METABOLISM                       0.31268448 -0.315035601  0.02591551  0.453707816 -0.07827502  0.12111801  0.4400906  0.15739138 -0.34124605 -0.0079268025  0.045340682  0.11082758 -0.26167624  0.22159523  0.249023937 -0.267370796  0.21778307  0.26025801 -0.171924064 -0.24608881 -0.26204891 -0.28320893 -0.0131339608 -0.174961467 -0.39051601 -0.27174210  0.21371632  0.004495443  0.07795065  0.141105313 -0.08136747  0.09135035 -0.2760584617  0.3120288128 -0.422743981  0.010521260
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM  0.04284560  0.242702474 -0.16024204  0.043647596  0.40725858  0.02861019  0.0869175  0.08096997 -0.05586613 -0.2040867733 -0.079009204 -0.30416447 -0.02979989  0.11484475  0.310350471 -0.167737512  0.02286110  0.02643017  0.079373530 -0.12361833  0.09011634  0.03828625 -0.2567878942  0.216249675 -0.26035482 -0.15309936  0.26950126  0.340594005 -0.28467469  0.223281462 -0.05508784  0.11421331 -0.0221915154 -0.3103008655  0.128094123  0.236156967
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM     0.24472652 -0.281133287 -0.11156638  0.120281095  0.17443484 -0.21565939 -0.3081781 -0.11343483  0.31456894 -0.1543122886 -0.174461409  0.00981391 -0.39082192  0.15162090  0.304717020 -0.014069234  0.02620582 -0.23568881  0.193879486 -0.13962369 -0.14580659  0.28040853 -0.0968041965  0.295147940  0.20766864 -0.09101975  0.19914336 -0.142750362 -0.06039776  0.529969819 -0.28971540 -0.01846407 -0.0650840198 -0.3562492770  0.352102978  0.244584623
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM          0.46919646 -0.380168943 -0.01773872  0.429812246  0.17364178 -0.20436261  0.3043864  0.34337161 -0.38080508  0.0857564710 -0.259409275 -0.05096080 -0.18249829  0.51288839  0.190289996 -0.436378420  0.26664702 -0.04414401  0.003940629 -0.49894385 -0.19574616 -0.05029689 -0.1798573066 -0.187265879 -0.11896302 -0.27828650  0.06494072  0.013637116 -0.27060418  0.395741143 -0.20169400 -0.05662690 -0.2624484362  0.0223987576 -0.151832657  0.296253623
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION   0.13275992 -0.334172234 -0.25729613  0.213014739  0.16552566 -0.28549989  0.5557899 -0.12594035 -0.32547571 -0.0907632515  0.375179490 -0.05918342  0.18499723  0.52187226  0.300515960 -0.433259137  0.36300112  0.23581480 -0.253354935 -0.24446632 -0.23069885 -0.30728634 -0.1095251897  0.335974432 -0.42786720 -0.35467130  0.05607809 -0.014724657 -0.38384764  0.189365161  0.32880955 -0.10650837 -0.2283860731 -0.0006837462 -0.011463264  0.281658787
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS  0.35031536 -0.131098230 -0.53101140  0.415024947  0.45022902  0.07344530  0.2667975 -0.21350030 -0.37419888 -0.6434244295  0.073570259 -0.16930988 -0.19093678  0.44377540  0.326753030 -0.395315587  0.20165887 -0.22843625 -0.345896575  0.21733136 -0.03379007 -0.33373706 -0.5598750406  0.105668958 -0.11338129 -0.25640184  0.53293944 -0.179140993 -0.15447191  0.309858597  0.28568125 -0.55068386 -0.2164372037 -0.1388932338  0.141542931  0.095210761
KEGG_LYSINE_DEGRADATION                          0.18631105 -0.302707855  0.14202963 -0.001457447  0.05052599  0.13664666  0.3353993  0.17015808 -0.15999281  0.0003802554  0.054289069 -0.06841515  0.19332597  0.06780524  0.394846160 -0.308209809  0.06840594 -0.30368912  0.173959126 -0.20656156 -0.14215812 -0.10346628  0.1434771096  0.077612666 -0.18316752 -0.05935752  0.15458897 -0.072955358 -0.26549273 -0.117408842  0.01486245 -0.19612153 -0.3691316847  0.0986933555  0.018713137  0.172759177
KEGG_ARGININE_AND_PROLINE_METABOLISM             0.27398245 -0.007553433 -0.20383827  0.190912564  0.26352645 -0.08892086  0.3364975  0.08336217 -0.15782044 -0.0366667890 -0.011447268 -0.19979109  0.07225283  0.30484966  0.104227507 -0.292574794  0.28948741  0.07959214  0.004233241 -0.25695797 -0.29744163  0.17250236 -0.1975298264  0.243301838 -0.25109237 -0.11660031  0.11820678  0.051556447 -0.24134955  0.339674687  0.03932339  0.11905051 -0.1702678011 -0.1936881912 -0.061558207  0.052832710
KEGG_HISTIDINE_METABOLISM                        0.32955287 -0.058544393  0.23401842  0.171291998  0.01579836  0.04289179  0.1478472 -0.19081266  0.10636274  0.0513523626 -0.227789459 -0.12657552 -0.23705948  0.17255355  0.063928642 -0.080957390  0.35225566  0.03053317  0.084445528 -0.09753282 -0.25255017  0.15575959  0.0462057297  0.127088199 -0.15801348 -0.39696091 -0.45105115  0.434357500 -0.03828497  0.050745235 -0.09141518  0.34481527  0.0778549056  0.1205808645  0.113071962 -0.107230492
KEGG_TYROSINE_METABOLISM                        -0.01013158 -0.196595442 -0.32598629  0.237374402 -0.23250901  0.20262459  0.2232565  0.26627457 -0.23842877  0.1924628476 -0.246173912 -0.11841733 -0.42705595  0.01951022  0.004484624  0.007798831  0.38715574  0.09743186 -0.182999776  0.20096611  0.40982753  0.05350491 -0.3214152163  0.182897748 -0.31135667 -0.45610097  0.33612797  0.127951123  0.29610319 -0.171090713  0.15670333 -0.08207433  0.2424991314 -0.0314562499  0.083631130  0.152278634
KEGG_PHENYLALANINE_METABOLISM                    0.18148770  0.461371608 -0.62020227 -0.140393277  0.27692153 -0.20565575 -0.2649484  0.10789494 -0.12695163 -0.1941535369 -0.595583680 -0.09085442 -0.46311485 -0.44379258 -0.093990808  0.280938193  0.09934493 -0.08162794  0.486358071 -0.06639144  0.37934632  0.56113507 -0.1060230711  0.468069197 -0.17744056 -0.17662290  0.14870307  0.649119193  0.19443272 -0.290354517 -0.55479111  0.45091097  0.3370977631  0.1944685634 -0.125721282 -0.096339449
KEGG_TRYPTOPHAN_METABOLISM                       0.02655589  0.043109593 -0.31856690  0.098466690  0.13008831 -0.18630463  0.2146807  0.05227151  0.09215733 -0.1502355445  0.007752516  0.06575941  0.14715900  0.31087022  0.208518310 -0.129119060  0.15933118 -0.11659123  0.158404342 -0.40413725 -0.29996492  0.20866768 -0.0003029911  0.127581506 -0.15098840 -0.26429807 -0.09215367  0.330810321 -0.29378958  0.015665134 -0.06172804  0.33048668  0.0406671480 -0.0549421996 -0.009869338 -0.070819327
> 
> gbmPar <- gsvaParam(gbm_eset, brainTxDbSets, maxDiff=FALSE)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
                    TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up                -0.3047539          -0.2946860          -0.1834593          -0.5442776          -0.2834175          -0.2788147          -0.3003514          -0.2874994           0.2607199           0.1413387           0.2146940          -0.3180027          -0.4002297           0.1769516          -0.2588480          -0.3482341          -0.2662723          -0.3459269          -0.4173384          -0.1983332          -0.1586231          -0.3486947          -0.3458663          -0.2206452           0.2825297          -0.3877544           0.2093004          -0.2012996          -0.3454799           0.1747717          -0.1457140           0.1895460          -0.2553038          -0.3954264          -0.1289837          -0.3769329          -0.4737155          -0.3632470          -0.3043683           0.2444025          -0.3233087          -0.4249789          -0.3426041          -0.2380239          -0.3075525          -0.3459151          -0.3087816           0.2381330          -0.2643738          -0.2797349
astroglia_up                 -0.5149583          -0.5410770          -0.4707559          -0.6113382          -0.4302575          -0.3653708          -0.4790737          -0.4724831           0.2019720          -0.5165498          -0.3810421          -0.4003590          -0.3525063          -0.4778482           0.1594521          -0.2744265          -0.4668132          -0.5181954          -0.4725050           0.3496106           0.1632234          -0.5350220          -0.5062797          -0.5565810          -0.2063866          -0.4462150          -0.1671050          -0.4503466          -0.5630672          -0.4053433           0.1609667          -0.1794776          -0.4755774          -0.2128034          -0.1997192          -0.5332830          -0.4417129          -0.4310179          -0.4982304           0.2722387          -0.3527572          -0.4120461          -0.5092322           0.1534758          -0.3638957          -0.2886322          -0.3058095          -0.2268245          -0.3789481          -0.4199315
neuronal_up                   0.5535049           0.2417091          -0.2419423          -0.1264513           0.5321516          -0.1907802          -0.3594715           0.3119123           0.4301345          -0.1251531           0.6345184          -0.4761376          -0.4777196          -0.3691534           0.2468458          -0.3802419           0.4236358          -0.4473820          -0.1168248           0.2615203           0.4412960           0.2258959           0.4605784          -0.1201504          -0.2601714          -0.2213066           0.5831010          -0.3449359          -0.3518502           0.1186366           0.1916525          -0.3076000           0.3498210           0.4973920           0.6397865          -0.2787217           0.2572456           0.4607110           0.3686673           0.1846618           0.5245801          -0.3509494           0.3513964           0.5454430           0.1606448          -0.2953076          -0.5303268           0.6995543           0.1475983          -0.1844540
oligodendrocytic_up           0.3317492           0.2491713           0.3353197           0.1965032           0.4766178           0.3696743           0.1739008           0.2837137           0.3965796          -0.2499617           0.4111354           0.3145638           0.6296969           0.3363415          -0.1374640           0.4114245          -0.3041959           0.2647537           0.4139883           0.2318300           0.3873472           0.2032636           0.4537419           0.2660245           0.5308132           0.4464649           0.5707848           0.3329401           0.4571077           0.2958584           0.3318632           0.4968947           0.3523085           0.5364637           0.4087340           0.5468353          -0.1492890           0.4105960           0.5855587          -0.1819342           0.4798445          -0.1856330          -0.1874635           0.4959465           0.5271533           0.2206708           0.2340045           0.2860177           0.1995836           0.1418165
                    TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up                -0.4388712          -0.2984390          -0.2418500           0.2967027           0.2963262           0.5497730           0.2387450           0.3144786           0.3333460           0.2297994           0.2686543           0.2357884           0.3223822           0.2434233           0.4129700           0.3558037           0.2586949           0.2957692          -0.1293295           0.4002767           0.2431737           0.2064763          -0.2054680           0.2098025           0.2378884           0.1979041           0.2823311           0.1955658           0.3445508           0.2594091           0.2529872           0.4826020           0.1815513           0.4318795           0.2885936           0.3123410          -0.3779783           0.1939708           0.1641413           0.1497425           0.2281183           0.1198567           0.3737903           0.2232357           0.2131509           0.2635626           0.2295927           0.2025863           0.3654367           0.3070467
astroglia_up                 -0.5577897          -0.3009622          -0.4952939           0.3562099          -0.1948617           0.2506709          -0.1956322           0.2980680           0.1473354           0.1866536          -0.4623550          -0.1714237          -0.4221490          -0.1818365          -0.2457673           0.2500337          -0.2661463          -0.1506672          -0.4899183          -0.3467717           0.2013752          -0.1561121          -0.2157769          -0.2982904          -0.3172812          -0.2281312           0.2970433          -0.2815591           0.1634429          -0.1746780          -0.3294734          -0.2707020          -0.3002505           0.3839744           0.2305549          -0.1605050          -0.2294543           0.4619706          -0.1943197          -0.2982120          -0.2123044           0.3634887           0.2863492           0.3384878           0.1948430           0.1395315          -0.2248029          -0.2162429          -0.2067516          -0.3013420
neuronal_up                   0.2111547           0.1714030           0.4657383           0.5497687          -0.3946098           0.4963120           0.3352992           0.7175166           0.4972767           0.3710156           0.7631191           0.5344811           0.7969773           0.2856497           0.3129090           0.6442165          -0.2297751           0.4688783           0.7186127           0.1864052           0.1512623           0.4905083           0.5779253          -0.1747120           0.7386962           0.5896950           0.2983598           0.4279023           0.2145936           0.1761452          -0.5754318           0.4795529          -0.6007193           0.6585229           0.2712467          -0.5609244          -0.5409766          -0.5582310          -0.1397818          -0.1699394           0.1369626          -0.2852583          -0.2074379          -0.3609699          -0.4746596           0.2723624          -0.1921239          -0.6249382          -0.1989687           0.4172576
oligodendrocytic_up           0.3666431           0.3008428           0.3834914          -0.2197493          -0.4632601           0.1755629           0.2283133           0.3855686          -0.1581432           0.2212679           0.2711446          -0.1950745           0.2557408           0.2960432          -0.1573391           0.3797065          -0.3338795          -0.2831008          -0.2227159          -0.1671839           0.4939055           0.1723784          -0.2516605          -0.1981382           0.3178961          -0.3937384          -0.2466558          -0.4638286          -0.4636637          -0.2714250          -0.3701235           0.2071280          -0.3779293          -0.3386804           0.2197589           0.2601284          -0.3611962           0.1908298          -0.4231171          -0.3430255          -0.3512123          -0.2820085          -0.3780724          -0.3704518          -0.3216412          -0.3171512          -0.2142009          -0.2771720          -0.1908734          -0.1300848
                    TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up                 0.4009205           0.3415409           0.2219087           0.2208367           0.2603907          -0.1765010           0.2940235           0.2124375           0.4061779           0.4328053           0.2173015           0.3551808           0.2219615           0.4042258           0.3642527           0.3044645           0.3551091           0.4812290          -0.2947330           0.2717050          -0.2072296          -0.2471975          -0.2842497           0.3991259          -0.2766075          -0.1677575          -0.2641184          -0.1595722           0.1984901          -0.2226697           0.1713801          -0.2188904          -0.2579632           0.1518073           0.1637208           0.3756718           0.2550845           0.1295303          -0.2700193           0.2063444           0.1624008          -0.3704812          -0.2729261           0.1962416          -0.1590410           0.3119768           0.2627011           0.2888753           0.2002931          -0.1400612
astroglia_up                 -0.2684818          -0.2478927           0.4042948           0.2335354          -0.4561683          -0.2852517           0.2751976           0.3726306           0.3118150          -0.2394383           0.1820660          -0.2988110           0.1652119           0.1841336           0.2581383           0.2056429          -0.2597831           0.3690882           0.4820315           0.2887467           0.5403445           0.4579650           0.5444281           0.5331769           0.3394440           0.2194871           0.5238034           0.4465451           0.4552118           0.3171873           0.5092584           0.4264341           0.3355302           0.4395682           0.3572217           0.5354133           0.5529363           0.3635790           0.4608111           0.3641927           0.4291813           0.4496740           0.4566347           0.3510896           0.4412179           0.3601076           0.3276640           0.5528990           0.4514321           0.2932687
neuronal_up                   0.4714021          -0.5453959          -0.2184275          -0.6205832           0.3765956          -0.4810052          -0.3898214          -0.3376351           0.4026263           0.2958724           0.1514880          -0.5448607           0.4816556          -0.5156220          -0.5857302          -0.3912544          -0.4810045          -0.4432014          -0.3401462          -0.2069768          -0.1755817          -0.5429475          -0.3473447           0.4293285          -0.1852551          -0.2807897           0.2095081           0.1692813          -0.5953110          -0.4569613           0.4986510           0.6780347          -0.4361162          -0.2657947          -0.4149003          -0.2019748          -0.1825776           0.4705841          -0.3660470          -0.3950770          -0.2875748          -0.3687514          -0.4339034          -0.4137328          -0.4061838          -0.3665761          -0.2886278          -0.4494102          -0.4614783           0.3012511
oligodendrocytic_up          -0.2170210          -0.3505377          -0.4033821          -0.4180423          -0.4282208          -0.4921075          -0.3129745          -0.2568446          -0.4508574          -0.3521717          -0.1932037          -0.2401757          -0.4705363          -0.4756500          -0.3939968          -0.4508653          -0.4673510           0.6267838          -0.3869379          -0.1753464           0.1398180          -0.3356724           0.2174792          -0.1909474          -0.4170448          -0.3449788          -0.3789635          -0.3723979          -0.2489271          -0.2955629           0.2563263           0.5062260          -0.3722382          -0.2544347          -0.4120718           0.1481816           0.2266027           0.2624142           0.6390087           0.1041047          -0.3246204          -0.2504649           0.1695500           0.3362893           0.2602318          -0.4512150          -0.2275365          -0.4490874           0.2728064           0.1801245
                    TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up                -0.3141722           0.2699874           0.2219473           0.2091188           0.2345999          -0.2194917          -0.3453076          -0.4238358           0.3549822           0.2340566          -0.2593196           0.1099604          -0.2273672           0.2019316          -0.2041700          -0.1508235          -0.2519564           0.1867464          -0.1965190           0.2585439          -0.3990271          -0.3061357           0.1651281
astroglia_up                  0.3922137           0.2846455           0.4656351           0.5682138           0.4886159           0.3895400           0.3730679           0.2343013           0.4820948           0.3943550           0.4396104           0.5514612           0.4772503           0.5054087           0.5478562           0.3711037           0.3050986           0.2872253           0.2808018           0.5497252           0.4051805           0.4516472           0.4085658
neuronal_up                  -0.4367833          -0.3295978          -0.2846818          -0.4517050          -0.3885191          -0.3608320          -0.3779686          -0.3484378          -0.2868552          -0.5719856          -0.2625708           0.2935293          -0.3335214           0.6340333          -0.4788773           0.5079833           0.1255322           0.2449831          -0.5029271          -0.3891953          -0.3632664          -0.4659142          -0.2670667
oligodendrocytic_up          -0.1680797           0.2981662          -0.4332569          -0.2097164          -0.4411032          -0.4515751          -0.1344606          -0.2894701          -0.3966829          -0.3681011          -0.2038674          -0.1537039           0.2336640          -0.2932406          -0.2495044           0.2091980          -0.3179201          -0.3245650          -0.2703005          -0.4534530          -0.4265475          -0.4192150           0.1600080
> 
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+                                 grep("_DN$", names(c2BroadSets)))]
> leukPar <- gsvaParam(leukemia_eset, cgpC2BroadSets,
+                      minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
                                                  CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP                     -0.284185921         0.09894281        -0.09166085         0.15556858        0.018687701         0.21589856       -0.159760678        -0.39128861        -0.26727234        -0.44679630        0.325744327        -0.23951518        0.051302632       -0.278506974         0.04015073        0.347632324        -0.24804097        -0.38938143        -0.15524618         0.19043913         0.02370623        0.068903997        -0.29422954         0.36158458        0.322237127       -0.075044727         0.18750433         0.22546588       -0.150244738       -0.132861970        0.245771407        0.253424577        0.149179429        0.256834003         0.54585089        -0.13771429       -0.381283518
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP                     0.074234671         0.28539841         0.54867983        -0.21455850       -0.196029929        -0.25981972        0.473892865         0.08132092        -0.02781303         0.54530761        0.366563615         0.32206336       -0.020333305       -0.304173959         0.16484183        0.025761275         0.04010094         0.12058207        -0.28234199        -0.32765526         0.33755016        0.062136062        -0.17438543        -0.27714732       -0.175368929       -0.068632830        -0.16029136        -0.54312340       -0.457243901        0.063838909        0.284048174        0.451910696        0.065458637       -0.216675403        -0.09964422        -0.46293573       -0.471055266
WINTER_HYPOXIA_UP                                       -0.122226539         0.19658831         0.19027777        -0.19779261       -0.295049369        -0.24808384       -0.216814893        -0.14968164        -0.14439647         0.16117004       -0.263075768         0.24300974        0.212753169        0.219567220        -0.26389007        0.067029667        -0.06856209        -0.08909042        -0.05226506        -0.30733660         0.22533379        0.193092854         0.04216994        -0.27030754        0.146503383        0.248352494        -0.08507045         0.02799035       -0.019718990        0.163757054        0.226094520        0.147465095        0.144632935       -0.177600100        -0.03490205        -0.02579216       -0.201473546
PYEON_HPV_POSITIVE_TUMORS_UP                             0.373338180        -0.08195895         0.49691537        -0.35523689        0.073820829         0.08656391        0.257900378         0.52264452         0.40765416         0.46023184        0.085547216         0.57035112       -0.453573874        0.127033813         0.41338035       -0.144148442         0.34650611         0.42161444         0.05076537        -0.50755967         0.06858839       -0.122209941         0.14630225        -0.46393255       -0.297018214       -0.007595085        -0.17430019        -0.34867040        0.238611621       -0.485707594       -0.393180984        0.283583934       -0.117141935       -0.264746769        -0.50063635        -0.42226439        0.030286161
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP             0.034852372         0.17810998         0.33466738        -0.18043537       -0.301630159        -0.25696203        0.069464046        -0.13728252         0.03289923         0.15662255        0.008254385         0.17876533       -0.035728864        0.263860776         0.18841806        0.054449457        -0.05893731        -0.03627519        -0.02106037        -0.30409556         0.26346145       -0.033555920        -0.09904109        -0.31073293        0.196059298        0.041943377        -0.27670124         0.05374531        0.102078549        0.089751050        0.126164281        0.073107504        0.159604038        0.149992036        -0.17339221        -0.12806055       -0.183128694
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP                -0.297408395         0.12039801        -0.26428063         0.17004586       -0.039805152         0.09850287       -0.057298350        -0.35386190        -0.16713553        -0.07892505        0.200098274        -0.20933571        0.144977450       -0.026805809         0.09893933       -0.004404619        -0.15285474        -0.30327609        -0.06851817         0.09694832        -0.24544948        0.118722964        -0.34259752         0.15768732        0.172784905       -0.184720574         0.19647116         0.20367723       -0.143437960        0.203937367        0.294431435        0.184358331        0.272106482        0.260812933         0.29031258         0.18633750       -0.058307777
LU_TUMOR_VASCULATURE_UP                                 -0.303485092         0.05954910        -0.08947968         0.17393748        0.055216604        -0.21711694       -0.068811743        -0.36596763        -0.10701941        -0.26356696        0.360410658        -0.07864957       -0.121613155        0.177822010        -0.01104916        0.229093881        -0.18613941        -0.27316309         0.12995187         0.27171808        -0.30894560        0.172438331        -0.30343314         0.37190436        0.180795286       -0.104016386        -0.07390340         0.21484484       -0.372653361        0.272063159        0.146426458        0.292726824        0.073215278        0.236064108         0.12233488         0.30677400       -0.166297976
KORKOLA_EMBRYONAL_CARCINOMA_UP                          -0.237891606         0.22324873         0.36244453        -0.10961418       -0.136474592        -0.46990350       -0.273764475        -0.16989735        -0.22372057         0.11247316       -0.232337649         0.28697934        0.017986838        0.142356962        -0.07127081        0.189358376         0.18951708         0.36031203        -0.18122486        -0.25323494         0.42996355        0.240702262         0.14655134        -0.29879857       -0.105909705       -0.186176950        -0.23520759         0.11808592        0.123806950       -0.096186587        0.082449346        0.068290275        0.204362056       -0.305158509        -0.18242290         0.07924085        0.050412994
KORKOLA_TERATOMA_UP                                      0.069466630         0.31282751         0.26793152         0.09145777        0.364378105        -0.01610294       -0.429410344        -0.34268743        -0.49321544        -0.29390567       -0.294556431        -0.43171623       -0.275085564       -0.198360712         0.34983219        0.320807082         0.13961117        -0.13440310         0.10165153         0.12248119         0.32044205        0.106653855         0.01837852         0.25031318       -0.310896163        0.053773795         0.03604947         0.33071217        0.066562201        0.280163027        0.039476681       -0.126383734        0.241910733       -0.323470237        -0.03914776         0.30954031        0.103077314
KORKOLA_YOLK_SAC_TUMOR_UP                                0.165072940         0.38624888         0.50530097        -0.37418563        0.006252226        -0.41666427       -0.301013273        -0.13354266        -0.14397323         0.31804861       -0.080548556         0.23290348        0.035345111        0.007931487        -0.09467101       -0.158566311         0.29400647         0.34421179        -0.14156018        -0.16187218         0.22342054        0.257582308        -0.07203685        -0.28296980       -0.390797184       -0.299345198        -0.33442798        -0.05640545       -0.267890012       -0.360997781        0.046532067       -0.038161214        0.260330724       -0.286721001        -0.29560478         0.25567578       -0.058961842
KORKOLA_CHORIOCARCINOMA_UP                              -0.010233903         0.32695285         0.23409239        -0.44995947        0.110491619        -0.77486388       -0.590305245        -0.30294240        -0.37350003         0.22506301       -0.122120864         0.36713585        0.321071992       -0.025352644         0.18055781        0.006019335         0.33689753         0.01559227        -0.39322807        -0.49057169         0.60777944        0.563917133         0.23716208        -0.44914903       -0.257199360        0.181773354        -0.26429369         0.34875870       -0.418331961       -0.402954949        0.279270709       -0.219024970       -0.073131401       -0.377126885        -0.01449304         0.08204518        0.009841082
KORKOLA_SEMINOMA_UP                                     -0.298212257         0.01080115         0.24405821        -0.15938874       -0.027952932        -0.28780633       -0.247319424        -0.33519149         0.06014085         0.22168793        0.058430886         0.28316538       -0.005576346        0.060208089         0.07375198       -0.081445539         0.16610491         0.42430320        -0.01533883         0.08230093         0.24992576        0.077656272        -0.06562014        -0.16684190       -0.284188016       -0.287282092        -0.16462701        -0.05811647       -0.062401658       -0.099243073        0.073201955        0.067154795        0.267030362       -0.298357838         0.02900301         0.32555350        0.080225727
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP        0.097593813        -0.16794685         0.35151193        -0.23237964       -0.163197206        -0.29950843       -0.006714904         0.34062208         0.09604888        -0.11003744       -0.171064434         0.06587775       -0.266062516        0.220122655         0.33608928       -0.127916894         0.11383392         0.19988434         0.20190981        -0.30021326         0.14299295        0.063923084         0.05677644        -0.28986580        0.038510117       -0.159509213        -0.29388778         0.05765373        0.326704138        0.074522409       -0.274247777       -0.275056415        0.053402889       -0.002107284        -0.34859857         0.03644107        0.208732689
HOLLMAN_APOPTOSIS_VIA_CD40_UP                            0.105496299        -0.13988837         0.38579893        -0.24564927       -0.083118397        -0.02283095        0.141139992         0.25611563        -0.05713898         0.01803229       -0.087474542         0.14542629       -0.210191344        0.211687858         0.22093653       -0.133326040         0.06549381         0.18478682        -0.03775017        -0.20148605         0.22321211       -0.059252095         0.01426428        -0.09291203       -0.005412103       -0.025056156        -0.28678304        -0.10392565        0.206300949        0.073580108       -0.204915942       -0.221567934       -0.045463659        0.033396194        -0.24875118         0.01892772        0.157710229
LIU_PROSTATE_CANCER_UP                                  -0.224388256         0.06307335        -0.08241727        -0.04832687        0.189906903        -0.02124567       -0.279030644        -0.27886322        -0.09392327        -0.19792744       -0.029580432        -0.03027978        0.202657103       -0.340883536        -0.03209933       -0.116168855        -0.30287655         0.21450416        -0.04221989        -0.04528200         0.06964423        0.083598831         0.16642355         0.12185052       -0.000928352        0.140595272         0.28592176         0.02379778       -0.071982214        0.154329444        0.077278879        0.239783535        0.316168936        0.045907958         0.11350734         0.06778064       -0.142535169
LIU_SOX4_TARGETS_UP                                      0.121044935        -0.14068822         0.22940559        -0.01597795        0.061591507        -0.00693642        0.014199778         0.30911203        -0.08600822        -0.02038572        0.114287917        -0.21978031       -0.226307014       -0.023607467         0.29166627        0.064022632         0.06822989        -0.07130524         0.23335358         0.06981417        -0.11573705       -0.291602661        -0.13629614        -0.03270145        0.024218801       -0.013336764        -0.10693992        -0.16558042        0.190828338        0.225771717       -0.229823064       -0.164944356       -0.179080910        0.177092706        -0.17646028        -0.18791880        0.240962021
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP            0.062841657        -0.18362789         0.29336781        -0.18594491        0.154299300        -0.05557008       -0.083102532         0.04576576        -0.09217560        -0.19543518        0.055196463        -0.04809592       -0.052719541        0.107250567         0.17234102        0.220352187        -0.04953385         0.24873127         0.13828440         0.19314948         0.04975678        0.049538498        -0.06477196        -0.06226135       -0.098276136       -0.129915554        -0.19707557         0.02496088       -0.051271962        0.052870430       -0.073226448       -0.184972633       -0.012686096       -0.071808834        -0.27150226         0.27912570       -0.135303937
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP                -0.094846112        -0.07207493        -0.02804641         0.03696695       -0.086436392        -0.08397341       -0.068172639        -0.05763452        -0.02656466        -0.17775526        0.258308865        -0.14822566       -0.145150486       -0.039994112         0.10916677       -0.090893212         0.03680901        -0.09371656         0.11806513         0.17785724        -0.11045327       -0.058180594        -0.31826977         0.09626481        0.143735941       -0.160260444        -0.06107374         0.08258827        0.034945942        0.261716811        0.008073164       -0.089058343        0.056294586        0.251527056         0.01348282         0.28709952        0.102083930
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP                 0.074340051         0.02857125        -0.24003150         0.30715667       -0.010403308        -0.10045962       -0.159844495        -0.22324560         0.02880624         0.11715699        0.077777052        -0.17990167        0.106011986       -0.179976522        -0.09660455        0.026469354        -0.12555729        -0.17002077         0.19363609         0.07413777        -0.34472957        0.071120620        -0.23684660         0.25225819        0.214521242       -0.165874245        -0.03452474        -0.02439650       -0.180590309        0.011098030        0.114305528        0.052961087       -0.068405608        0.293293442         0.24643595         0.09297256       -0.030979738
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP                     0.005014724         0.08111308         0.26913235        -0.09552045       -0.450228901        -0.20835559       -0.341832089         0.08934729        -0.33423215        -0.07570491       -0.227456658        -0.31425832       -0.075046342        0.101225498        -0.22803411        0.359148102         0.25779762        -0.50524646         0.12655983        -0.08326589         0.16277302       -0.238058161        -0.17065282         0.06861909        0.125783171       -0.153453577        -0.06888951         0.35891268        0.238976848        0.449575492       -0.397721447        0.129949315        0.063354595        0.344276854         0.21919705        -0.02084416        0.446602851
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP                     -0.086490808         0.42662285        -0.06186335         0.19254225       -0.147417154         0.23175825        0.491914629        -0.11696009         0.01145265        -0.18617542       -0.098643515        -0.08071038       -0.040838732       -0.284554435         0.44402053       -0.167965862        -0.06796364        -0.12183172         0.37256760         0.34632681         0.01477953        0.154501865        -0.14155636        -0.17148626        0.040841265       -0.199318164        -0.03141871        -0.02556187       -0.194745034        0.111576773        0.299019277       -0.246935585       -0.304924920        0.249744542         0.16874813        -0.28320150       -0.409684665
FRASOR_TAMOXIFEN_RESPONSE_UP                             0.095102205         0.13613061         0.27963248         0.10696680       -0.201251938         0.04440738        0.039666191         0.08072985        -0.30347286        -0.13117213       -0.163829152        -0.08811162        0.130289925       -0.269491251         0.04481561       -0.129982372        -0.09261704         0.05779261         0.20931794        -0.11293941        -0.08782228       -0.154603301        -0.10942582         0.03255269        0.068908002       -0.134879788        -0.11865894         0.03929191        0.105215621        0.144775760       -0.132818191       -0.126161041        0.046198277        0.066790819         0.10784581         0.14897625        0.103889267
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP                   -0.093263740         0.24451532        -0.30875436        -0.01171828       -0.077592391         0.06977365       -0.047698353        -0.25543630        -0.16734657        -0.29943342        0.138659259        -0.24677548        0.008316094       -0.097198227        -0.07991562        0.237943766        -0.08176618        -0.34607119         0.18984664         0.28121888        -0.29765020        0.006609358        -0.17838613         0.18555511        0.093828022       -0.218609231         0.17434097         0.06804717       -0.095062879        0.199580074        0.321860622       -0.008284166       -0.001916854        0.183088620         0.25305607         0.13585610        0.034581179
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP                     0.203957767         0.12189117         0.38492132        -0.24300464       -0.090523098        -0.19966713        0.102728363         0.04976671         0.18283638         0.30437400        0.148109727         0.24724848       -0.327248458        0.129670458         0.33143975       -0.086102559         0.10335793         0.20068518         0.03773511        -0.23454620         0.13617294       -0.090673447        -0.26073243        -0.38875239       -0.054723088       -0.050551494        -0.23180710        -0.12601589       -0.001883262       -0.007476349        0.072573918        0.189048383        0.090254301        0.187420576        -0.31338258        -0.10912037       -0.247410905
WATANABE_COLON_CANCER_MSI_VS_MSS_UP                     -0.156524705        -0.00167507        -0.10689295         0.36427412       -0.010218876        -0.06496857       -0.269749963        -0.27745767         0.02119152        -0.21830558       -0.196574719        -0.35120814        0.269162954       -0.142483756        -0.26808257        0.038724466        -0.07004319        -0.11588327        -0.10292213        -0.06427425         0.25284346        0.283925446         0.01040659         0.32549432        0.230151042        0.409316724         0.37175290        -0.27673142       -0.066751401       -0.078279396        0.099369827       -0.165196141        0.013360644        0.168730310         0.23632001        -0.18337713       -0.329485400
> 
> proc.time()
   user  system elapsed 
 66.346   3.474  69.814 

GSVA.Rcheck/tests/test_gsva_newapi.Rout.save


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> 
> ## 2023-11-10  axel: simple test script for method GSVA, new API
> 
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    expand.grid, I, unname

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db


> library(GSVA)
> 
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
> 
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
> 
> p <- 10000 ## number of genes
> n <- 30    ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+             dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
           s1         s2          s3         s4          s5
g1  1.4171739 -1.3444519 -0.99052898  0.4203395  1.30716224
g2 -0.7281951  0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754  0.09779699 -0.6792548 -0.09124045
g4  1.0735382  1.3156255  0.15588330 -1.8079608  0.48531108
g5  0.7229884 -0.9162342  1.93982245  0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+                    paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> gsvaPar <- gsvaParam(X, gs)
> gsva.es <- gsva(gsvaPar, verbose=FALSE)
> dim(gsva.es)
[1] 100  30
> gsva.es[seq.int(min(nRowsToPrint, nrow(gsva.es))),]
               s1          s2           s3          s4          s5            s6           s7           s8           s9          s10          s11          s12         s13          s14          s15          s16          s17          s18          s19         s20          s21          s22         s23          s24         s25           s26           s27          s28          s29         s30
gs1  -0.108156444  0.16592613 -0.143808928  0.11391879 -0.08600850 -0.1734242744  0.178707342  0.017723667  0.094198786  0.103231011  0.098990086  0.056687452 -0.19582109  0.012296862  0.162223446 -0.114766326 -0.293330673  0.126367035  0.228829622 -0.14884956  0.026620947 -0.301784054 -0.30631599  0.235331985  0.04638816 -0.1100099596 -0.0999704513 -0.046424755  0.293447378 -0.17344608
gs2  -0.078540545  0.19300391  0.079182716  0.07049058  0.04007773  0.1715072044  0.203277577 -0.081465590  0.233451158 -0.280324459  0.037382517  0.025061259  0.10845168 -0.059159170  0.026844586 -0.179610527 -0.014413382 -0.006820970  0.160768137 -0.03932893 -0.108749046 -0.282019527  0.08605189  0.088382420  0.06394081  0.0207049280  0.2183498851  0.084518747 -0.272555793 -0.17000646
gs3  -0.012507633 -0.25351738  0.102368361  0.03512929 -0.04994980  0.2133058738  0.039178136  0.191682501 -0.398094428  0.343111543 -0.076791958  0.119069468  0.20772960 -0.421116272  0.459538877 -0.026465562  0.049041138  0.038384015 -0.227781747 -0.09134458 -0.514150386  0.102494298 -0.20024782  0.058491931  0.31836609  0.0290482835 -0.1935787866  0.254416177 -0.017322981  0.13715416
gs4  -0.083248846  0.02946102 -0.042556750  0.08145113 -0.05401867  0.1055847509 -0.158661388  0.009278808 -0.107756958 -0.016141791 -0.033233344  0.016122676 -0.08342913 -0.003621483  0.141048462 -0.001454018  0.129386313 -0.062100704 -0.110927318 -0.16530100 -0.059697155  0.032076675  0.03158162  0.038234047 -0.03942766  0.0886365597 -0.0782910850  0.014516781 -0.046885905  0.20075530
gs5   0.129917233 -0.14323749 -0.172890947  0.13411529  0.09628743  0.0265475253  0.050870369  0.174122516  0.081836827 -0.011085820  0.023089550  0.056006287 -0.07140253  0.055193034 -0.091548680 -0.149492965  0.037312222  0.002985924 -0.144101863 -0.01888358 -0.065961297 -0.132468115 -0.06377434  0.028402402 -0.07610908  0.0853809151  0.0806035221 -0.015568714 -0.047153650  0.01778386
gs6  -0.284972014  0.13823428 -0.210772112 -0.05757943  0.10388699  0.1439391564  0.109157571  0.077447106  0.001144118  0.181326976 -0.019716350 -0.006386486 -0.06006467 -0.189315716  0.005405993 -0.001953525  0.006055122  0.159361735 -0.089341440  0.02743543  0.000728224 -0.178928406  0.19578172 -0.036394549 -0.07703071  0.0784321711 -0.0863070990 -0.033617568 -0.088131880  0.09008523
gs7   0.028701964  0.23235456  0.119915418 -0.01970966 -0.13698294  0.0031401764 -0.218020511 -0.195273449  0.038952752 -0.232984107  0.037413398  0.092363954  0.18259907  0.053162383  0.097674825 -0.128073348  0.073567722  0.115641271  0.030537867 -0.13049139 -0.057022525  0.056026838  0.06828574 -0.001000666 -0.06071745  0.0039744122 -0.0005585096 -0.009440488  0.080790372 -0.09940113
gs8   0.006333045  0.01460128  0.136198133 -0.07889863 -0.11123825  0.0387444491 -0.002037746  0.040187847 -0.121686486 -0.095484760  0.052264970  0.150236692  0.04926308 -0.109888308  0.100412242  0.146400621 -0.156050604  0.018922498  0.067657595 -0.05343596 -0.068927042 -0.080941576  0.07501949  0.007660285  0.16079137 -0.2682601362  0.1012140737  0.042776107  0.002111495 -0.05482992
gs9  -0.175865699 -0.19690763  0.060751759  0.18933359 -0.25345038 -0.5016097134 -0.138854281 -0.543295516 -0.263543869  0.275493131  0.127068488 -0.189846149 -0.25784051 -0.094258279  0.079039460 -0.165487585  0.343543465  0.357424759  0.292115383 -0.02178526  0.058171774 -0.034552813  0.23880691  0.043569142 -0.02980941  0.2945856247 -0.0219706361 -0.176772536  0.532204432  0.15142975
gs10  0.098112170 -0.35611542 -0.056579211 -0.21958226  0.08809195  0.0009137342  0.405507850 -0.115481827 -0.187608357  0.275280555 -0.119567715  0.109071314 -0.25466878  0.000375529  0.367963754  0.188641874 -0.079209335  0.256239935 -0.125622141 -0.11854834  0.255106701  0.471876454 -0.37385722  0.223837887  0.02289076 -0.4287911223  0.0067681070 -0.240476346  0.088671730 -0.17764056
gs11  0.098198198  0.25911849 -0.038035464 -0.21771367  0.50403680  0.4428564710  0.303629955  0.175137764  0.098749107  0.336354436  0.130586418 -0.052651015 -0.20599477 -0.223219535 -0.250927738 -0.509205728 -0.444857809 -0.045479124  0.088547534 -0.02722749 -0.099107700 -0.092392768  0.05594057 -0.069222681 -0.02071750 -0.5973180441 -0.1580304020  0.577149382  0.298070860 -0.07458713
gs12  0.096490065 -0.02605933 -0.022030360 -0.13719093  0.02682772  0.0434813048 -0.028867424  0.014475285  0.133723333  0.034558185  0.137695531 -0.258037193 -0.02835015 -0.064346101 -0.026710216 -0.269826308  0.021532017 -0.047943462 -0.022440279  0.16687604  0.055835937  0.023685654 -0.06486901 -0.020025683  0.02178566  0.0480895384  0.1113867112  0.059878337 -0.055779061  0.06729589
gs13  0.223982459  0.20679601  0.258716670 -0.20136940 -0.20071529  0.2464442479  0.258963232 -0.110149641 -0.089442650  0.205739275 -0.165291846 -0.150888458 -0.15226578 -0.404364664 -0.005312768 -0.100572023 -0.220803462 -0.043370760  0.309185329 -0.08715961  0.326811093  0.080713114 -0.10705436  0.116977351  0.19046277 -0.1469583728  0.1367810954 -0.242162288 -0.021163531 -0.29632096
gs14  0.024001674 -0.26723135 -0.398236422  0.24294428  0.04991522 -0.1433770344  0.399168882 -0.248011836 -0.121856855 -0.141859978 -0.080548602  0.105372091  0.28663719  0.303516623  0.320574969 -0.044182057 -0.177554197 -0.058580934  0.063071784  0.11623764  0.096538164 -0.055513833 -0.42073250  0.001550673  0.16488985  0.0464015474 -0.0156188987 -0.085775207 -0.160086709  0.12477191
gs15  0.107236756  0.02674424  0.186569862 -0.12214378 -0.06518532 -0.0612943018 -0.111903203  0.049803938  0.044035633 -0.049752082 -0.024069020  0.205529366 -0.10569735  0.002119758 -0.140742436  0.185481189 -0.005853900 -0.101479169 -0.001425559  0.08308067  0.020882554  0.051697561  0.05197634  0.276490515  0.09494653 -0.1604533503 -0.1106884939 -0.115292890 -0.212477678 -0.04261664
gs16 -0.189661090  0.18212481 -0.194291062  0.11967900 -0.10434220 -0.1191397416  0.039057392 -0.039343595 -0.060222683 -0.067506938 -0.160259179  0.001722109  0.14378774 -0.013559159  0.165627072 -0.022929924 -0.032725397 -0.021268004 -0.036164578  0.04105859  0.054069320 -0.023626997  0.01312951 -0.066479935  0.03594310  0.0510113983  0.0168947880 -0.006306806  0.182001699  0.08182702
gs17 -0.224154710 -0.06839924  0.011942989  0.06596303 -0.01898285 -0.0787236017  0.262432764  0.128350415  0.107171841 -0.036418415  0.004430908 -0.152391953  0.13910575 -0.034949755  0.129033846 -0.096575805  0.027781998  0.086966986 -0.057041784  0.06413185 -0.088718911  0.119981085  0.07640730 -0.116205119 -0.19211361  0.0949234199 -0.0301489984  0.007364308 -0.021454055 -0.05405507
gs18  0.144462699  0.15190319 -0.005644637  0.13442504 -0.06851005 -0.0650767309  0.132965207 -0.072143414  0.065609258 -0.169604968  0.149226527 -0.127080390  0.15127334  0.001524110 -0.096672404  0.138052662  0.156721335 -0.113260460 -0.055010361 -0.11281271 -0.081498926 -0.062627336  0.01138976  0.083051492 -0.11650835 -0.0644334115  0.0158668194 -0.035534584 -0.216520795  0.25451909
gs19 -0.114727405  0.11606640  0.014639537 -0.04539144 -0.15632885 -0.3008348682 -0.045227873  0.057911106  0.077993588  0.122127072  0.004180167 -0.010181304 -0.13058749 -0.017522472 -0.063018173  0.096067773  0.059813582 -0.042255247 -0.110140982  0.28341206 -0.057751403 -0.062970017 -0.26428505 -0.087882907 -0.06031966  0.2005231419  0.0555096129 -0.119697294  0.158883568  0.13631818
gs20 -0.250434807 -0.04667705  0.049213711  0.05304980  0.15123353  0.1091531262  0.061807069 -0.184158384  0.116516282 -0.024996495  0.050439116  0.062684587 -0.03915131 -0.056457080 -0.298840942  0.163262104 -0.029174994  0.169067340  0.055693074  0.03338657  0.068733916  0.047318574  0.05085801  0.007052938 -0.13510237 -0.0802436967 -0.0251620082 -0.048587104 -0.071021904 -0.04269538
gs21  0.135378868  0.16802591 -0.029364914 -0.05595578  0.06148837  0.0971278669  0.093694989 -0.069804459  0.025767351 -0.016170741 -0.101534883 -0.120160395  0.04062725  0.048721679  0.095192931 -0.186471874 -0.048112890 -0.212895052 -0.006971640 -0.06755367 -0.127602218 -0.002382844 -0.01605748 -0.001335954 -0.11991648  0.2219113569  0.1352495887  0.023381243  0.045687474  0.09964681
gs22 -0.163680317  0.18690317 -0.148456673 -0.05079516  0.24365056 -0.0822628950  0.098769260 -0.142649660 -0.444454723  0.065727715  0.247342235 -0.167215276  0.14197399  0.112681184 -0.092957822 -0.152497158 -0.190680030  0.035186284 -0.035122161  0.07290296  0.002562072  0.032535170  0.26649228  0.318514935 -0.22440917 -0.0178361034 -0.3138866671  0.416817320 -0.314242601 -0.02772554
gs23  0.018766631  0.11521514 -0.014809625  0.06153311  0.12707575  0.1281180662 -0.064456890 -0.030536563 -0.129612935 -0.015034995  0.129955588  0.057111134 -0.22165829  0.160845001  0.108799691  0.090243195  0.008299278  0.041996865  0.155112600 -0.08959788  0.079998925  0.013571384 -0.27985106 -0.134362071  0.05587958  0.0900157601 -0.0306708210 -0.124824057 -0.125258066  0.03409850
gs24  0.389869244  0.28790219 -0.049088266 -0.14811747 -0.19067680 -0.3358219719 -0.236811755  0.135616593 -0.238985451  0.206904619  0.248194834 -0.112405472  0.09072771 -0.142415602 -0.383217061  0.363554498  0.187395921 -0.327457108 -0.592050113  0.15802933  0.479729800 -0.150610477  0.28243874 -0.202986917  0.12126635  0.0007700638 -0.0280707676  0.049077412 -0.212219932  0.12363971
gs25  0.093907002 -0.08177613  0.137542184  0.01817976 -0.07335024 -0.2779884851 -0.010150488 -0.109990320 -0.023037802 -0.006390004  0.088013029 -0.003651291 -0.16541049  0.090206786 -0.091065047  0.089689390  0.061729248  0.223324387  0.050045901 -0.08299866  0.221155832 -0.246784249  0.32074709  0.037550027 -0.16709326 -0.1213934826  0.1061837744  0.016007278  0.065201658 -0.19524119
> 
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+                     featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+                     sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+                                       grep("^REACTOME", names(c2BroadSets)),
+                                       grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- gsvaParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+                       minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
                                                    NA19099       NA18523      NA19144     NA19137      NA18861     NA19116     NA19130     NA19131      NA19119     NA19152       NA19153     NA19140      NA19138     NA18522      NA19192     NA19193     NA19239      NA19238      NA19210      NA19201     NA19172      NA18870     NA18858     NA18852     NA19159      NA18855     NA19204      NA18501     NA19127      NA19098      NA19093      NA18856       NA18912     NA18517      NA18502      NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                 -0.14418012 -3.133817e-01 -0.391171673  0.21340339  0.398980386 -0.03179434  0.17524757  0.26705934  0.196519789  0.07076882  0.0145998761  0.27413667  0.083361420 -0.10575923 -0.189608055 -0.30624818 -0.25363521 -0.371666584  0.131382543  0.122449569  0.19101441 -0.452577261 -0.23105310  0.10274129  0.13624827 -0.007124138  0.15976388 -0.102152201 -0.19832123  0.202573385  0.378578854  0.288352608  0.0016120367 -0.36268281  0.110141001  0.255205365
KEGG_CITRATE_CYCLE_TCA_CYCLE                    -0.20263269  2.546732e-01  0.012685194 -0.23423639  0.166963123 -0.19060735 -0.09504444  0.02350579  0.252153864 -0.29870033  0.3426900775  0.11865360  0.158070942  0.43950013 -0.113554675 -0.41027161 -0.51496205  0.101464045  0.023147027  0.213518494 -0.29129288 -0.365361233  0.19537441  0.34046332 -0.29053602 -0.136804277 -0.03945536 -0.046177552 -0.15861718 -0.197363503  0.005305269  0.139063426  0.3753961988 -0.11672606  0.399275124  0.081808177
KEGG_PENTOSE_PHOSPHATE_PATHWAY                   0.13384996 -3.426199e-01  0.011055653  0.10473591  0.533196442  0.08319882 -0.07286230  0.33986046  0.183712674 -0.02112598  0.3436817431  0.14970027  0.045619795  0.34106103 -0.319187004 -0.12337277 -0.52047602 -0.079296210  0.246091695  0.007442165  0.29667112 -0.493628865 -0.37567090  0.04398852 -0.10380781 -0.066433829  0.07248245 -0.134640505 -0.28388477 -0.007933863 -0.010660832  0.409249866 -0.0593083889 -0.20730184  0.135344012  0.328985231
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS   -0.04814412  2.649390e-01 -0.247781616 -0.57051071 -0.151893395 -0.12257602 -0.22484133  0.15415444  0.170044654 -0.41770107  0.4059486427  0.32600904 -0.337637004  0.45224654  0.240860923 -0.52860069  0.06878373  0.238734193  0.199127444  0.197382585  0.19194776 -0.280713555 -0.14573199 -0.07489534 -0.17115751 -0.356340540  0.19199016  0.464332824 -0.30954147  0.066784875  0.107764195 -0.244087607 -0.0038072528 -0.15577831  0.159465388  0.173314410
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM            -0.05277464 -2.559473e-01 -0.272606595  0.02654463  0.466256330 -0.07516578 -0.08827428  0.17940166  0.175438074  0.08335115  0.1949276528  0.03263319 -0.037187373  0.21769233 -0.056026638 -0.21875825 -0.41789351 -0.167172773 -0.116119580  0.028778964  0.18475990 -0.006106045 -0.35983263  0.04835565  0.13058334  0.320582420  0.14792337 -0.356458053 -0.32573808 -0.200330955  0.256816456  0.243425591  0.1799096212  0.04042810  0.078246331  0.111827102
KEGG_GALACTOSE_METABOLISM                       -0.51060398 -3.263793e-01 -0.339445527  0.18058711  0.590147665 -0.05433206 -0.02631533  0.01150479  0.112418121  0.20086931  0.0758757516  0.18135031  0.172899748  0.09960453 -0.419887121 -0.30998273 -0.41031657 -0.552555465  0.134889700  0.312990925  0.40442648 -0.314101297 -0.45866474  0.24674708  0.36744079 -0.300764693  0.46807677 -0.119986976 -0.47812839 -0.137744193  0.179487063  0.362685887 -0.1178698280 -0.27717714  0.333123866  0.570589012
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM           0.39533716  1.058190e-01 -0.055948980  0.32042238  0.117469296 -0.47857258 -0.27397801  0.48975038 -0.092440191 -0.05795173 -0.0744286061 -0.21729660  0.193086799  0.31390769  0.038143586  0.04976352  0.06941386 -0.243260211 -0.075892533 -0.136936205 -0.70456483 -0.248431863  0.04441643  0.16407617  0.10523266  0.201548537 -0.63041976 -0.064796304 -0.42586995  0.071454531  0.327254119 -0.007811551  0.2006101479  0.02592733 -0.340917460  0.307433176
KEGG_FATTY_ACID_METABOLISM                       0.03299573  1.864144e-01  0.209909423 -0.24436698  0.207945636 -0.12244431 -0.23816823  0.49912101  0.388462885 -0.20945911  0.0991996326  0.28644900  0.027816218  0.13251193 -0.076840810 -0.35401475 -0.26281629  0.022061212  0.092216454  0.131207009 -0.32302048 -0.043107375 -0.17671170  0.13894499 -0.29064351 -0.119433589 -0.42265454 -0.103764267 -0.09629923 -0.114672086  0.246246155  0.137119878  0.4886075270 -0.07587824  0.017144468  0.033774833
KEGG_STEROID_BIOSYNTHESIS                        0.19815359 -1.774636e-01 -0.495105675 -0.25914877  0.190294265 -0.32446562  0.40274807  0.55575502  0.334577780 -0.30738356  0.0995344990  0.02714295 -0.341505856  0.33481474  0.483575947 -0.46782536 -0.41070981  0.363247663 -0.316476327  0.186672062  0.06775463 -0.460614122 -0.03811347  0.10403630  0.19161113 -0.276517655 -0.31751788 -0.335291201  0.04610323  0.498441393  0.203641470  0.258537460  0.1025848927  0.32986280  0.106728771  0.044375942
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS             -0.22772338  3.313823e-01 -0.045122587  0.34604215 -0.326387527 -0.37238068  0.38109784  0.50612839 -0.279733901 -0.46710624 -0.3566433892  0.38150788 -0.160181485  0.32343792 -0.389633800 -0.04093348 -0.34781666  0.439898619 -0.553153746  0.333311581 -0.41569720  0.089984351  0.11640121  0.49616048 -0.18515617 -0.288891006 -0.25307258  0.488505183  0.48932043  0.685621131  0.405112800 -0.410676806  0.0705999647  0.46798357 -0.050407919 -0.059580749
KEGG_STEROID_HORMONE_BIOSYNTHESIS                0.36585090 -4.158145e-02 -0.314872488  0.36177011 -0.117186424 -0.57565233  0.06555161  0.12421684 -0.154537531 -0.03651661  0.2548932547 -0.25983105 -0.191491808 -0.01727654  0.007925232  0.20173611  0.07385251 -0.151691776 -0.174246389  0.170112989 -0.31138189 -0.287770962 -0.32224067  0.25539717  0.10328113 -0.240352841 -0.02844086  0.115892938  0.20532852  0.092026010  0.444749927  0.138675375 -0.1017217201  0.19796954 -0.321674802  0.386149959
KEGG_OXIDATIVE_PHOSPHORYLATION                  -0.44614351  4.066706e-01  0.315683836 -0.38414333 -0.062919018  0.19858654 -0.22582769  0.04161922 -0.079644512 -0.05102341  0.3664592628 -0.09619084  0.197886790  0.31353680 -0.184933831 -0.36350759 -0.30233809  0.313796606  0.236200087 -0.322015323 -0.29790565 -0.196993574 -0.08707882  0.26462100 -0.24626717  0.241984062  0.12731683 -0.209160519 -0.13913537 -0.164019798  0.003657569  0.174518566  0.2846868562 -0.03739754  0.351418754 -0.151465743
KEGG_PURINE_METABOLISM                          -0.12658061  6.074446e-05  0.109942629  0.02507931  0.152633778  0.20438698  0.05049747  0.08805693 -0.163334045 -0.09018816  0.2671088095  0.13157027  0.002135794  0.19941825 -0.014318164 -0.19467600 -0.19570945  0.160038352 -0.003976608 -0.159354533  0.04953516 -0.237144513 -0.19729598  0.06518253 -0.20013531  0.065168510 -0.02813078  0.001056042 -0.03466977 -0.006764599  0.054072961 -0.010634495  0.1220901659 -0.14216130  0.002592869 -0.079175937
KEGG_PYRIMIDINE_METABOLISM                      -0.08169375  2.124920e-02  0.237112503  0.02740654 -0.007840300  0.24898451 -0.04095103  0.23335111 -0.156235016 -0.16193850  0.2906078400  0.19091514 -0.095748971  0.19881417  0.039922114 -0.17823010 -0.14678724  0.256232748  0.020947130 -0.088582706  0.16161796 -0.307232427 -0.08240158  0.03008501 -0.30460678  0.090542640 -0.09034804 -0.174657514 -0.09426947 -0.129635921 -0.040660453 -0.066351934  0.3336055751 -0.05856322 -0.032156131 -0.179871004
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM -0.13254287 -6.225182e-02 -0.134319540 -0.15729012  0.026834849 -0.22343907  0.14168564  0.30713913 -0.125172326 -0.17862058 -0.1731094263  0.30055821 -0.085420317  0.09882301  0.193697084  0.31425985 -0.31600195 -0.125372528  0.295397875  0.180199556 -0.20500280  0.058617241 -0.14777995  0.05091438  0.12367397 -0.040310943 -0.08013473  0.182346297 -0.10198293  0.197362551  0.285434513  0.083269169 -0.3708006909 -0.06111266 -0.243366412  0.222746237
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM     0.10719371 -4.606961e-01 -0.180567057  0.09540174  0.245012608 -0.15656927  0.22420420  0.05451998  0.279637623  0.13353399  0.0588075025 -0.29202943 -0.043946876  0.01212064  0.153895823  0.41802493 -0.13778592 -0.372235469 -0.406109789  0.283133835  0.19519783 -0.020078578 -0.26407215  0.12285472  0.26704639  0.059250879  0.04897781 -0.250007490 -0.05255973  0.087369877  0.196707759  0.202125900 -0.4079062250 -0.14271079  0.201471466  0.148775715
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM          0.31199860 -1.470030e-01  0.003351767  0.19314634 -0.069733318  0.03818098  0.14330053  0.29773728  0.199561609 -0.18575435  0.2414974155  0.26605667 -0.291208656  0.16923947  0.350632975  0.15181300 -0.22743772 -0.019995533  0.165918443 -0.282999158  0.23210130 -0.390498560  0.09366624 -0.22502795 -0.10851096 -0.372625112 -0.43938185  0.172251073  0.03236597  0.169871903 -0.116676657 -0.006200565 -0.2279015972 -0.18233790  0.215082562 -0.127529151
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION   0.13690035  3.114732e-01  0.066312869 -0.42482813 -0.090282754  0.17692622 -0.19729696  0.34694241  0.407012719 -0.49732087  0.4128185814  0.21841977  0.209032500  0.22079194  0.098804076 -0.28545919 -0.23815839 -0.180999045  0.227212036  0.266627679 -0.26343085 -0.365422361 -0.24682867  0.09025547 -0.26797947 -0.355998344 -0.48059599  0.287997010  0.04787260  0.218397773  0.054137782 -0.098018435  0.3267593437 -0.45818263  0.271972064  0.296388858
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS  0.21018404  3.311632e-01 -0.305891231 -0.40884425  0.154601400  0.29113672 -0.24105148 -0.24181442  0.181954325 -0.58092775  0.4049453421  0.24614645  0.133009367  0.50265059  0.272676320  0.03717033 -0.02236702 -0.145501442  0.138011286  0.443984308  0.39650468 -0.290692301 -0.12632929 -0.19057616 -0.07228556 -0.257796347  0.05090257 -0.239289854 -0.27079693 -0.411150458  0.112237525 -0.264314957 -0.4438365768  0.26411102  0.709862664 -0.016572984
KEGG_LYSINE_DEGRADATION                         -0.05052662  1.114498e-02  0.229382702  0.09046133  0.038741982  0.28814839 -0.18110222  0.18668860  0.200429660 -0.15730855  0.2122002799  0.15678305  0.291243079 -0.09136060  0.075543036 -0.20498916 -0.11109630 -0.119030450 -0.042852292  0.236306523  0.07759842 -0.290175631 -0.01746742 -0.21890493 -0.20792480  0.077495323 -0.27615714  0.039431840 -0.12276895 -0.053898732 -0.080541817 -0.016639943  0.0009973473 -0.40134082  0.137262457  0.007682097
KEGG_ARGININE_AND_PROLINE_METABOLISM            -0.22800596  4.906206e-02 -0.042335265  0.01804139  0.185198410 -0.31622084  0.33887630  0.14716659 -0.125964421 -0.04372424 -0.1317531626 -0.23684263 -0.084937438  0.12230128  0.041463950  0.01888723 -0.23867163 -0.418034734  0.100108084 -0.024241225  0.06662724  0.062701077 -0.18005295  0.28126338  0.26487393  0.117918976  0.03282485 -0.267823209 -0.11043893  0.310700224  0.208244241  0.293517379 -0.1408712737  0.08681285  0.022305834  0.089895339
KEGG_HISTIDINE_METABOLISM                        0.36390137  2.365551e-01 -0.116603139 -0.05003836  0.327736448 -0.21045969 -0.09444006  0.07411204  0.004241093 -0.21347825 -0.2759296517 -0.09004815 -0.220892221 -0.04865282  0.223799615  0.07800378  0.10695352  0.008719129 -0.157708191 -0.206105926 -0.07079359  0.329843813 -0.03292310 -0.12534816  0.15073847 -0.369373567 -0.44170643  0.302626017 -0.35207965  0.319661614  0.084963193 -0.328337412  0.0562137944 -0.01801214 -0.140975452 -0.224081075
KEGG_TYROSINE_METABOLISM                         0.20007757  1.721769e-01 -0.037643348 -0.19625928 -0.075882501 -0.12591313  0.33248542 -0.07760137 -0.191628836 -0.18678014  0.0004931861 -0.41470470 -0.197618861  0.44585904  0.460970463 -0.23734373  0.06323644  0.447147523 -0.339999748 -0.263094997  0.32393110  0.148291697 -0.02476993 -0.16845439 -0.05628810 -0.228433500 -0.09241908  0.205241359 -0.14005676 -0.123163041  0.280135889 -0.404510468 -0.0076082103  0.41987347  0.046111365 -0.109788331
KEGG_PHENYLALANINE_METABOLISM                    0.14876060  3.091885e-01 -0.425309307  0.03290077  0.007314721 -0.44139027  0.41683218  0.00264260 -0.665142859  0.33683691 -0.1354678721 -0.56429899 -0.339302707  0.23461582  0.388641234 -0.14178018 -0.13963600  0.402700359 -0.060552296  0.198533242  0.30608114 -0.367173008  0.39977893  0.09861950  0.19457836 -0.450408082  0.02414787  0.419408775  0.14007478 -0.167643347  0.038509810 -0.118899152 -0.4538199574  0.58568820  0.155660090 -0.409252364
KEGG_TRYPTOPHAN_METABOLISM                       0.02771378  7.276144e-02  0.164993365 -0.04842795  0.275480475 -0.39691784 -0.07428901  0.25507776  0.187930224 -0.16961352 -0.0772668699  0.10285172 -0.067196121  0.10898541 -0.204308026 -0.07494849 -0.14783141 -0.200577850  0.338704351  0.030157577 -0.38063449 -0.187786425  0.04954516 -0.07650680  0.08969431 -0.024503220 -0.28162674  0.105474846 -0.15358250 -0.063342825  0.059069680 -0.027357901  0.4168932938  0.08101763 -0.197098915  0.014085911
> pickrellPar <- gsvaParam(pickrellCountsArgonneCQNcommon_eset,
+                          canonicalC2BroadSets, minSize=5, maxSize=500,
+                          kcdf="Poisson")
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esrnaseq)[seq.int(min(nRowsToPrint, nrow(esrnaseq))),]
                                                    NA19099      NA18523     NA19144      NA19137     NA18861     NA19116    NA19130     NA19131     NA19119       NA19152      NA19153     NA19140     NA19138     NA18522      NA19192      NA19193     NA19239     NA19238      NA19210     NA19201     NA19172     NA18870       NA18858      NA18852     NA19159     NA18855     NA19204      NA18501     NA19127      NA19098     NA19093     NA18856       NA18912       NA18517      NA18502      NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                  0.22920126 -0.264187722 -0.37401687  0.291350766  0.17081880 -0.45702585  0.5003620 -0.09626897 -0.47879477  0.2009603094  0.092846463  0.39386860 -0.10064875  0.25767347 -0.006960737 -0.323002689  0.54088138  0.36740468 -0.230653742 -0.21517689 -0.39153412 -0.10416424 -0.0260882429  0.206128783 -0.38394575 -0.26111852  0.11124358 -0.307607156 -0.23108674  0.118623744  0.40568230 -0.35928390 -0.2287986403  0.0674126870 -0.194909729  0.406279736
KEGG_CITRATE_CYCLE_TCA_CYCLE                     0.19534471 -0.202157014 -0.31886736  0.257353003  0.09452472 -0.14337654  0.5803541  0.21971004 -0.48460389 -0.0910376333  0.143073239 -0.01343428  0.21924711  0.14911562  0.331156020 -0.623445470  0.26517213  0.10217269 -0.244826732 -0.08275136 -0.13342326 -0.18991201  0.2222643203 -0.008264954 -0.27726336 -0.32626055  0.55391119 -0.274223459 -0.41600613 -0.239476881  0.23644605 -0.33329094 -0.4140553740  0.3505474463 -0.034676768 -0.002314262
KEGG_PENTOSE_PHOSPHATE_PATHWAY                   0.39571823 -0.352221233 -0.14016244  0.358512977  0.16414025 -0.26589439  0.6674822  0.17953342 -0.55049088  0.0562838685  0.021675321  0.57648156  0.11371008  0.29864451  0.104942610 -0.504014044  0.57693561  0.46862262 -0.257288782 -0.36529987 -0.33598186 -0.39358598  0.1109189257  0.023878095 -0.34214747 -0.25852067  0.28121726 -0.435798801 -0.31480707 -0.007553482  0.26670234 -0.45518879 -0.4532774636  0.2948129840 -0.267281290  0.463433745
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS    0.30431379 -0.234295884 -0.27059673 -0.245346011 -0.06027442  0.04706860  0.3884300 -0.15945758  0.02075130 -0.0008356316  0.156613047 -0.06726357 -0.25892817  0.47051857  0.358948273 -0.512413738  0.41386623  0.25956799  0.146563139 -0.10384415  0.29375249 -0.32605966 -0.3406774353 -0.079363956 -0.25850079 -0.55407022  0.33385389  0.468934430 -0.03022371  0.104853773  0.29678304 -0.14204144  0.3091341703 -0.0449204187 -0.269151573  0.118249851
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM             0.11231761 -0.062748045 -0.04494400  0.443120939 -0.43879510 -0.26298245  0.4742617  0.10248633 -0.35537405  0.1685276920  0.144103617  0.21438430  0.15584943  0.01726953  0.220675430 -0.319381715  0.48892920  0.46105569 -0.426727337 -0.19856115 -0.31952483  0.01320194 -0.0382402740 -0.043511121 -0.35219578 -0.12906627  0.26969235 -0.290367845 -0.32181822 -0.242589300  0.35793456 -0.18587339 -0.3767879009  0.3985766414 -0.191002663  0.343416703
KEGG_GALACTOSE_METABOLISM                        0.06062020 -0.424855520 -0.03930301  0.349652791 -0.12188569 -0.46296074  0.5180153 -0.01789657 -0.35356594  0.2446797481  0.473003017  0.34499007  0.34112213  0.25024239  0.250381767 -0.453215048  0.57769569  0.21561858 -0.337261669 -0.08753488 -0.42331301 -0.04093081 -0.2210103855  0.056226416 -0.07839585  0.07879640  0.27290820 -0.414140702 -0.36050412 -0.191532611  0.39567826 -0.53298775 -0.4127888920  0.3440494486 -0.178365423  0.513262262
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM           0.51820705  0.039968658 -0.12377878 -0.036122904  0.31985771 -0.46527398  0.3988617  0.01038232  0.37687330  0.5270758669 -0.001642410 -0.11679805 -0.05628187  0.71772103  0.241534280 -0.289882381  0.69553991  0.45968207  0.296411226 -0.50738472 -0.41554732 -0.27269571 -0.0503383811  0.414487589 -0.23400690 -0.52790283 -0.51602401  0.445718811 -0.42330633  0.174908837 -0.07311759  0.34397307  0.2085765041 -0.3221300091 -0.392502279  0.284751348
KEGG_FATTY_ACID_METABOLISM                       0.20886138 -0.242876900 -0.30320811  0.187550569  0.29327773 -0.08700294  0.5230685  0.27380231 -0.34116554  0.1472345229  0.062594388  0.08687790  0.14291551  0.51283780  0.291434806 -0.504476008  0.43294161  0.28219716 -0.304791635 -0.30535668 -0.18442492 -0.13244662  0.0150691534  0.283488006 -0.48289609 -0.49976986  0.09652311 -0.011347711 -0.31278105  0.239631877  0.20679322 -0.03829960 -0.3295649579 -0.0001742616 -0.141024787  0.339491609
KEGG_STEROID_BIOSYNTHESIS                        0.33604553  0.078851347 -0.52590310 -0.263728541  0.32226372  0.07485904  0.3016156  0.28921483 -0.28561530 -0.6241643849 -0.150031690 -0.31567564  0.10600143  0.12621865  0.040239055 -0.372783352 -0.17192551 -0.02763554 -0.362917924 -0.33311374 -0.30449600 -0.19719698  0.6253409182 -0.008988029  0.19293398  0.09900056  0.13681999 -0.119518167 -0.26419274 -0.013995204  0.20395478  0.11325134  0.1626070916  0.5348477961  0.511074525 -0.190211341
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS              0.15739882  0.084600205 -0.52857163  0.553659439  0.26308379 -0.59676812  0.1225233  0.47452481  0.39641389 -0.4648496916 -0.432446416  0.25929223  0.48938377 -0.03614696 -0.087619025 -0.409483402 -0.39069390  0.44383724 -0.217291058 -0.06841149 -0.20808586  0.30133475  0.2338089031  0.628743013 -0.21619683 -0.24904089 -0.29348796  0.201532148  0.37954912  0.371373220  0.35506241  0.16613077 -0.1045489108 -0.3541049382 -0.187847376  0.005129543
KEGG_STEROID_HORMONE_BIOSYNTHESIS                0.38438742  0.113162544 -0.45530979  0.357007701 -0.25621878 -0.29318119 -0.1569740  0.14898979  0.39668852 -0.0468902937 -0.117557120 -0.02018489  0.05524139  0.23740098 -0.066581664  0.258410115  0.10847272 -0.13068365 -0.211051369 -0.28866137 -0.15360410  0.38750091 -0.3238802927  0.274917265  0.25281933  0.01163520 -0.01972985  0.521392285  0.25890358 -0.202780567  0.14930619  0.49695425 -0.0003891365 -0.4015589637 -0.319750989  0.216079876
KEGG_OXIDATIVE_PHOSPHORYLATION                   0.03439798 -0.068230945 -0.24335287  0.179558503 -0.07748180  0.23899287  0.5355567  0.10928544 -0.58653812 -0.1232948723  0.011594465  0.25516015  0.10959538  0.23121819  0.196992997 -0.214021354  0.13140917  0.22589733 -0.167995266 -0.12327534  0.02643072 -0.11175039  0.0487111545 -0.293168402 -0.43460403 -0.36521148  0.06558919 -0.309035960  0.24113723 -0.186432466  0.25366326 -0.01546476 -0.1003451715  0.2488324612 -0.323304803 -0.197206582
KEGG_PURINE_METABOLISM                           0.20191160 -0.108479208 -0.10596002  0.292297651 -0.05290036 -0.02776887  0.3629813  0.19221693 -0.19257184 -0.1570618328  0.049458419  0.10941378 -0.11575356  0.10624767  0.139611752 -0.104415107  0.24845743  0.18074380  0.044016416 -0.21432408 -0.20002101 -0.17818482 -0.1294276990 -0.149379806 -0.20372875 -0.18695986  0.14562604 -0.027395894  0.03493636  0.032161754 -0.01145234  0.00244119 -0.1717349277  0.1040248755 -0.158512548 -0.016876129
KEGG_PYRIMIDINE_METABOLISM                       0.31268448 -0.315035601  0.02591551  0.453707816 -0.07827502  0.12111801  0.4400906  0.15739138 -0.34124605 -0.0079268025  0.045340682  0.11082758 -0.26167624  0.22159523  0.249023937 -0.267370796  0.21778307  0.26025801 -0.171924064 -0.24608881 -0.26204891 -0.28320893 -0.0131339608 -0.174961467 -0.39051601 -0.27174210  0.21371632  0.004495443  0.07795065  0.141105313 -0.08136747  0.09135035 -0.2760584617  0.3120288128 -0.422743981  0.010521260
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM  0.04284560  0.242702474 -0.16024204  0.043647596  0.40725858  0.02861019  0.0869175  0.08096997 -0.05586613 -0.2040867733 -0.079009204 -0.30416447 -0.02979989  0.11484475  0.310350471 -0.167737512  0.02286110  0.02643017  0.079373530 -0.12361833  0.09011634  0.03828625 -0.2567878942  0.216249675 -0.26035482 -0.15309936  0.26950126  0.340594005 -0.28467469  0.223281462 -0.05508784  0.11421331 -0.0221915154 -0.3103008655  0.128094123  0.236156967
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM     0.24472652 -0.281133287 -0.11156638  0.120281095  0.17443484 -0.21565939 -0.3081781 -0.11343483  0.31456894 -0.1543122886 -0.174461409  0.00981391 -0.39082192  0.15162090  0.304717020 -0.014069234  0.02620582 -0.23568881  0.193879486 -0.13962369 -0.14580659  0.28040853 -0.0968041965  0.295147940  0.20766864 -0.09101975  0.19914336 -0.142750362 -0.06039776  0.529969819 -0.28971540 -0.01846407 -0.0650840198 -0.3562492770  0.352102978  0.244584623
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM          0.46919646 -0.380168943 -0.01773872  0.429812246  0.17364178 -0.20436261  0.3043864  0.34337161 -0.38080508  0.0857564710 -0.259409275 -0.05096080 -0.18249829  0.51288839  0.190289996 -0.436378420  0.26664702 -0.04414401  0.003940629 -0.49894385 -0.19574616 -0.05029689 -0.1798573066 -0.187265879 -0.11896302 -0.27828650  0.06494072  0.013637116 -0.27060418  0.395741143 -0.20169400 -0.05662690 -0.2624484362  0.0223987576 -0.151832657  0.296253623
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION   0.13275992 -0.334172234 -0.25729613  0.213014739  0.16552566 -0.28549989  0.5557899 -0.12594035 -0.32547571 -0.0907632515  0.375179490 -0.05918342  0.18499723  0.52187226  0.300515960 -0.433259137  0.36300112  0.23581480 -0.253354935 -0.24446632 -0.23069885 -0.30728634 -0.1095251897  0.335974432 -0.42786720 -0.35467130  0.05607809 -0.014724657 -0.38384764  0.189365161  0.32880955 -0.10650837 -0.2283860731 -0.0006837462 -0.011463264  0.281658787
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS  0.35031536 -0.131098230 -0.53101140  0.415024947  0.45022902  0.07344530  0.2667975 -0.21350030 -0.37419888 -0.6434244295  0.073570259 -0.16930988 -0.19093678  0.44377540  0.326753030 -0.395315587  0.20165887 -0.22843625 -0.345896575  0.21733136 -0.03379007 -0.33373706 -0.5598750406  0.105668958 -0.11338129 -0.25640184  0.53293944 -0.179140993 -0.15447191  0.309858597  0.28568125 -0.55068386 -0.2164372037 -0.1388932338  0.141542931  0.095210761
KEGG_LYSINE_DEGRADATION                          0.18631105 -0.302707855  0.14202963 -0.001457447  0.05052599  0.13664666  0.3353993  0.17015808 -0.15999281  0.0003802554  0.054289069 -0.06841515  0.19332597  0.06780524  0.394846160 -0.308209809  0.06840594 -0.30368912  0.173959126 -0.20656156 -0.14215812 -0.10346628  0.1434771096  0.077612666 -0.18316752 -0.05935752  0.15458897 -0.072955358 -0.26549273 -0.117408842  0.01486245 -0.19612153 -0.3691316847  0.0986933555  0.018713137  0.172759177
KEGG_ARGININE_AND_PROLINE_METABOLISM             0.27398245 -0.007553433 -0.20383827  0.190912564  0.26352645 -0.08892086  0.3364975  0.08336217 -0.15782044 -0.0366667890 -0.011447268 -0.19979109  0.07225283  0.30484966  0.104227507 -0.292574794  0.28948741  0.07959214  0.004233241 -0.25695797 -0.29744163  0.17250236 -0.1975298264  0.243301838 -0.25109237 -0.11660031  0.11820678  0.051556447 -0.24134955  0.339674687  0.03932339  0.11905051 -0.1702678011 -0.1936881912 -0.061558207  0.052832710
KEGG_HISTIDINE_METABOLISM                        0.32955287 -0.058544393  0.23401842  0.171291998  0.01579836  0.04289179  0.1478472 -0.19081266  0.10636274  0.0513523626 -0.227789459 -0.12657552 -0.23705948  0.17255355  0.063928642 -0.080957390  0.35225566  0.03053317  0.084445528 -0.09753282 -0.25255017  0.15575959  0.0462057297  0.127088199 -0.15801348 -0.39696091 -0.45105115  0.434357500 -0.03828497  0.050745235 -0.09141518  0.34481527  0.0778549056  0.1205808645  0.113071962 -0.107230492
KEGG_TYROSINE_METABOLISM                        -0.01013158 -0.196595442 -0.32598629  0.237374402 -0.23250901  0.20262459  0.2232565  0.26627457 -0.23842877  0.1924628476 -0.246173912 -0.11841733 -0.42705595  0.01951022  0.004484624  0.007798831  0.38715574  0.09743186 -0.182999776  0.20096611  0.40982753  0.05350491 -0.3214152163  0.182897748 -0.31135667 -0.45610097  0.33612797  0.127951123  0.29610319 -0.171090713  0.15670333 -0.08207433  0.2424991314 -0.0314562499  0.083631130  0.152278634
KEGG_PHENYLALANINE_METABOLISM                    0.18148770  0.461371608 -0.62020227 -0.140393277  0.27692153 -0.20565575 -0.2649484  0.10789494 -0.12695163 -0.1941535369 -0.595583680 -0.09085442 -0.46311485 -0.44379258 -0.093990808  0.280938193  0.09934493 -0.08162794  0.486358071 -0.06639144  0.37934632  0.56113507 -0.1060230711  0.468069197 -0.17744056 -0.17662290  0.14870307  0.649119193  0.19443272 -0.290354517 -0.55479111  0.45091097  0.3370977631  0.1944685634 -0.125721282 -0.096339449
KEGG_TRYPTOPHAN_METABOLISM                       0.02655589  0.043109593 -0.31856690  0.098466690  0.13008831 -0.18630463  0.2146807  0.05227151  0.09215733 -0.1502355445  0.007752516  0.06575941  0.14715900  0.31087022  0.208518310 -0.129119060  0.15933118 -0.11659123  0.158404342 -0.40413725 -0.29996492  0.20866768 -0.0003029911  0.127581506 -0.15098840 -0.26429807 -0.09215367  0.330810321 -0.29378958  0.015665134 -0.06172804  0.33048668  0.0406671480 -0.0549421996 -0.009869338 -0.070819327
> 
> gbmPar <- gsvaParam(gbm_eset, brainTxDbSets, maxDiff=FALSE)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
                    TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up                -0.3047539          -0.2946860          -0.1834593          -0.5442776          -0.2834175          -0.2788147          -0.3003514          -0.2874994           0.2607199           0.1413387           0.2146940          -0.3180027          -0.4002297           0.1769516          -0.2588480          -0.3482341          -0.2662723          -0.3459269          -0.4173384          -0.1983332          -0.1586231          -0.3486947          -0.3458663          -0.2206452           0.2825297          -0.3877544           0.2093004          -0.2012996          -0.3454799           0.1747717          -0.1457140           0.1895460          -0.2553038          -0.3954264          -0.1289837          -0.3769329          -0.4737155          -0.3632470          -0.3043683           0.2444025          -0.3233087          -0.4249789          -0.3426041          -0.2380239          -0.3075525          -0.3459151          -0.3087816           0.2381330          -0.2643738          -0.2797349
astroglia_up                 -0.5149583          -0.5410770          -0.4707559          -0.6113382          -0.4302575          -0.3653708          -0.4790737          -0.4724831           0.2019720          -0.5165498          -0.3810421          -0.4003590          -0.3525063          -0.4778482           0.1594521          -0.2744265          -0.4668132          -0.5181954          -0.4725050           0.3496106           0.1632234          -0.5350220          -0.5062797          -0.5565810          -0.2063866          -0.4462150          -0.1671050          -0.4503466          -0.5630672          -0.4053433           0.1609667          -0.1794776          -0.4755774          -0.2128034          -0.1997192          -0.5332830          -0.4417129          -0.4310179          -0.4982304           0.2722387          -0.3527572          -0.4120461          -0.5092322           0.1534758          -0.3638957          -0.2886322          -0.3058095          -0.2268245          -0.3789481          -0.4199315
neuronal_up                   0.5535049           0.2417091          -0.2419423          -0.1264513           0.5321516          -0.1907802          -0.3594715           0.3119123           0.4301345          -0.1251531           0.6345184          -0.4761376          -0.4777196          -0.3691534           0.2468458          -0.3802419           0.4236358          -0.4473820          -0.1168248           0.2615203           0.4412960           0.2258959           0.4605784          -0.1201504          -0.2601714          -0.2213066           0.5831010          -0.3449359          -0.3518502           0.1186366           0.1916525          -0.3076000           0.3498210           0.4973920           0.6397865          -0.2787217           0.2572456           0.4607110           0.3686673           0.1846618           0.5245801          -0.3509494           0.3513964           0.5454430           0.1606448          -0.2953076          -0.5303268           0.6995543           0.1475983          -0.1844540
oligodendrocytic_up           0.3317492           0.2491713           0.3353197           0.1965032           0.4766178           0.3696743           0.1739008           0.2837137           0.3965796          -0.2499617           0.4111354           0.3145638           0.6296969           0.3363415          -0.1374640           0.4114245          -0.3041959           0.2647537           0.4139883           0.2318300           0.3873472           0.2032636           0.4537419           0.2660245           0.5308132           0.4464649           0.5707848           0.3329401           0.4571077           0.2958584           0.3318632           0.4968947           0.3523085           0.5364637           0.4087340           0.5468353          -0.1492890           0.4105960           0.5855587          -0.1819342           0.4798445          -0.1856330          -0.1874635           0.4959465           0.5271533           0.2206708           0.2340045           0.2860177           0.1995836           0.1418165
                    TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up                -0.4388712          -0.2984390          -0.2418500           0.2967027           0.2963262           0.5497730           0.2387450           0.3144786           0.3333460           0.2297994           0.2686543           0.2357884           0.3223822           0.2434233           0.4129700           0.3558037           0.2586949           0.2957692          -0.1293295           0.4002767           0.2431737           0.2064763          -0.2054680           0.2098025           0.2378884           0.1979041           0.2823311           0.1955658           0.3445508           0.2594091           0.2529872           0.4826020           0.1815513           0.4318795           0.2885936           0.3123410          -0.3779783           0.1939708           0.1641413           0.1497425           0.2281183           0.1198567           0.3737903           0.2232357           0.2131509           0.2635626           0.2295927           0.2025863           0.3654367           0.3070467
astroglia_up                 -0.5577897          -0.3009622          -0.4952939           0.3562099          -0.1948617           0.2506709          -0.1956322           0.2980680           0.1473354           0.1866536          -0.4623550          -0.1714237          -0.4221490          -0.1818365          -0.2457673           0.2500337          -0.2661463          -0.1506672          -0.4899183          -0.3467717           0.2013752          -0.1561121          -0.2157769          -0.2982904          -0.3172812          -0.2281312           0.2970433          -0.2815591           0.1634429          -0.1746780          -0.3294734          -0.2707020          -0.3002505           0.3839744           0.2305549          -0.1605050          -0.2294543           0.4619706          -0.1943197          -0.2982120          -0.2123044           0.3634887           0.2863492           0.3384878           0.1948430           0.1395315          -0.2248029          -0.2162429          -0.2067516          -0.3013420
neuronal_up                   0.2111547           0.1714030           0.4657383           0.5497687          -0.3946098           0.4963120           0.3352992           0.7175166           0.4972767           0.3710156           0.7631191           0.5344811           0.7969773           0.2856497           0.3129090           0.6442165          -0.2297751           0.4688783           0.7186127           0.1864052           0.1512623           0.4905083           0.5779253          -0.1747120           0.7386962           0.5896950           0.2983598           0.4279023           0.2145936           0.1761452          -0.5754318           0.4795529          -0.6007193           0.6585229           0.2712467          -0.5609244          -0.5409766          -0.5582310          -0.1397818          -0.1699394           0.1369626          -0.2852583          -0.2074379          -0.3609699          -0.4746596           0.2723624          -0.1921239          -0.6249382          -0.1989687           0.4172576
oligodendrocytic_up           0.3666431           0.3008428           0.3834914          -0.2197493          -0.4632601           0.1755629           0.2283133           0.3855686          -0.1581432           0.2212679           0.2711446          -0.1950745           0.2557408           0.2960432          -0.1573391           0.3797065          -0.3338795          -0.2831008          -0.2227159          -0.1671839           0.4939055           0.1723784          -0.2516605          -0.1981382           0.3178961          -0.3937384          -0.2466558          -0.4638286          -0.4636637          -0.2714250          -0.3701235           0.2071280          -0.3779293          -0.3386804           0.2197589           0.2601284          -0.3611962           0.1908298          -0.4231171          -0.3430255          -0.3512123          -0.2820085          -0.3780724          -0.3704518          -0.3216412          -0.3171512          -0.2142009          -0.2771720          -0.1908734          -0.1300848
                    TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up                 0.4009205           0.3415409           0.2219087           0.2208367           0.2603907          -0.1765010           0.2940235           0.2124375           0.4061779           0.4328053           0.2173015           0.3551808           0.2219615           0.4042258           0.3642527           0.3044645           0.3551091           0.4812290          -0.2947330           0.2717050          -0.2072296          -0.2471975          -0.2842497           0.3991259          -0.2766075          -0.1677575          -0.2641184          -0.1595722           0.1984901          -0.2226697           0.1713801          -0.2188904          -0.2579632           0.1518073           0.1637208           0.3756718           0.2550845           0.1295303          -0.2700193           0.2063444           0.1624008          -0.3704812          -0.2729261           0.1962416          -0.1590410           0.3119768           0.2627011           0.2888753           0.2002931          -0.1400612
astroglia_up                 -0.2684818          -0.2478927           0.4042948           0.2335354          -0.4561683          -0.2852517           0.2751976           0.3726306           0.3118150          -0.2394383           0.1820660          -0.2988110           0.1652119           0.1841336           0.2581383           0.2056429          -0.2597831           0.3690882           0.4820315           0.2887467           0.5403445           0.4579650           0.5444281           0.5331769           0.3394440           0.2194871           0.5238034           0.4465451           0.4552118           0.3171873           0.5092584           0.4264341           0.3355302           0.4395682           0.3572217           0.5354133           0.5529363           0.3635790           0.4608111           0.3641927           0.4291813           0.4496740           0.4566347           0.3510896           0.4412179           0.3601076           0.3276640           0.5528990           0.4514321           0.2932687
neuronal_up                   0.4714021          -0.5453959          -0.2184275          -0.6205832           0.3765956          -0.4810052          -0.3898214          -0.3376351           0.4026263           0.2958724           0.1514880          -0.5448607           0.4816556          -0.5156220          -0.5857302          -0.3912544          -0.4810045          -0.4432014          -0.3401462          -0.2069768          -0.1755817          -0.5429475          -0.3473447           0.4293285          -0.1852551          -0.2807897           0.2095081           0.1692813          -0.5953110          -0.4569613           0.4986510           0.6780347          -0.4361162          -0.2657947          -0.4149003          -0.2019748          -0.1825776           0.4705841          -0.3660470          -0.3950770          -0.2875748          -0.3687514          -0.4339034          -0.4137328          -0.4061838          -0.3665761          -0.2886278          -0.4494102          -0.4614783           0.3012511
oligodendrocytic_up          -0.2170210          -0.3505377          -0.4033821          -0.4180423          -0.4282208          -0.4921075          -0.3129745          -0.2568446          -0.4508574          -0.3521717          -0.1932037          -0.2401757          -0.4705363          -0.4756500          -0.3939968          -0.4508653          -0.4673510           0.6267838          -0.3869379          -0.1753464           0.1398180          -0.3356724           0.2174792          -0.1909474          -0.4170448          -0.3449788          -0.3789635          -0.3723979          -0.2489271          -0.2955629           0.2563263           0.5062260          -0.3722382          -0.2544347          -0.4120718           0.1481816           0.2266027           0.2624142           0.6390087           0.1041047          -0.3246204          -0.2504649           0.1695500           0.3362893           0.2602318          -0.4512150          -0.2275365          -0.4490874           0.2728064           0.1801245
                    TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up                -0.3141722           0.2699874           0.2219473           0.2091188           0.2345999          -0.2194917          -0.3453076          -0.4238358           0.3549822           0.2340566          -0.2593196           0.1099604          -0.2273672           0.2019316          -0.2041700          -0.1508235          -0.2519564           0.1867464          -0.1965190           0.2585439          -0.3990271          -0.3061357           0.1651281
astroglia_up                  0.3922137           0.2846455           0.4656351           0.5682138           0.4886159           0.3895400           0.3730679           0.2343013           0.4820948           0.3943550           0.4396104           0.5514612           0.4772503           0.5054087           0.5478562           0.3711037           0.3050986           0.2872253           0.2808018           0.5497252           0.4051805           0.4516472           0.4085658
neuronal_up                  -0.4367833          -0.3295978          -0.2846818          -0.4517050          -0.3885191          -0.3608320          -0.3779686          -0.3484378          -0.2868552          -0.5719856          -0.2625708           0.2935293          -0.3335214           0.6340333          -0.4788773           0.5079833           0.1255322           0.2449831          -0.5029271          -0.3891953          -0.3632664          -0.4659142          -0.2670667
oligodendrocytic_up          -0.1680797           0.2981662          -0.4332569          -0.2097164          -0.4411032          -0.4515751          -0.1344606          -0.2894701          -0.3966829          -0.3681011          -0.2038674          -0.1537039           0.2336640          -0.2932406          -0.2495044           0.2091980          -0.3179201          -0.3245650          -0.2703005          -0.4534530          -0.4265475          -0.4192150           0.1600080
> 
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+                                 grep("_DN$", names(c2BroadSets)))]
> leukPar <- gsvaParam(leukemia_eset, cgpC2BroadSets,
+                      minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
                                                  CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP                     -0.284185921         0.09894281        -0.09166085         0.15556858        0.018687701         0.21589856       -0.159760678        -0.39128861        -0.26727234        -0.44679630        0.325744327        -0.23951518        0.051302632       -0.278506974         0.04015073        0.347632324        -0.24804097        -0.38938143        -0.15524618         0.19043913         0.02370623        0.068903997        -0.29422954         0.36158458        0.322237127       -0.075044727         0.18750433         0.22546588       -0.150244738       -0.132861970        0.245771407        0.253424577        0.149179429        0.256834003         0.54585089        -0.13771429       -0.381283518
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP                     0.074234671         0.28539841         0.54867983        -0.21455850       -0.196029929        -0.25981972        0.473892865         0.08132092        -0.02781303         0.54530761        0.366563615         0.32206336       -0.020333305       -0.304173959         0.16484183        0.025761275         0.04010094         0.12058207        -0.28234199        -0.32765526         0.33755016        0.062136062        -0.17438543        -0.27714732       -0.175368929       -0.068632830        -0.16029136        -0.54312340       -0.457243901        0.063838909        0.284048174        0.451910696        0.065458637       -0.216675403        -0.09964422        -0.46293573       -0.471055266
WINTER_HYPOXIA_UP                                       -0.122226539         0.19658831         0.19027777        -0.19779261       -0.295049369        -0.24808384       -0.216814893        -0.14968164        -0.14439647         0.16117004       -0.263075768         0.24300974        0.212753169        0.219567220        -0.26389007        0.067029667        -0.06856209        -0.08909042        -0.05226506        -0.30733660         0.22533379        0.193092854         0.04216994        -0.27030754        0.146503383        0.248352494        -0.08507045         0.02799035       -0.019718990        0.163757054        0.226094520        0.147465095        0.144632935       -0.177600100        -0.03490205        -0.02579216       -0.201473546
PYEON_HPV_POSITIVE_TUMORS_UP                             0.373338180        -0.08195895         0.49691537        -0.35523689        0.073820829         0.08656391        0.257900378         0.52264452         0.40765416         0.46023184        0.085547216         0.57035112       -0.453573874        0.127033813         0.41338035       -0.144148442         0.34650611         0.42161444         0.05076537        -0.50755967         0.06858839       -0.122209941         0.14630225        -0.46393255       -0.297018214       -0.007595085        -0.17430019        -0.34867040        0.238611621       -0.485707594       -0.393180984        0.283583934       -0.117141935       -0.264746769        -0.50063635        -0.42226439        0.030286161
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP             0.034852372         0.17810998         0.33466738        -0.18043537       -0.301630159        -0.25696203        0.069464046        -0.13728252         0.03289923         0.15662255        0.008254385         0.17876533       -0.035728864        0.263860776         0.18841806        0.054449457        -0.05893731        -0.03627519        -0.02106037        -0.30409556         0.26346145       -0.033555920        -0.09904109        -0.31073293        0.196059298        0.041943377        -0.27670124         0.05374531        0.102078549        0.089751050        0.126164281        0.073107504        0.159604038        0.149992036        -0.17339221        -0.12806055       -0.183128694
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP                -0.297408395         0.12039801        -0.26428063         0.17004586       -0.039805152         0.09850287       -0.057298350        -0.35386190        -0.16713553        -0.07892505        0.200098274        -0.20933571        0.144977450       -0.026805809         0.09893933       -0.004404619        -0.15285474        -0.30327609        -0.06851817         0.09694832        -0.24544948        0.118722964        -0.34259752         0.15768732        0.172784905       -0.184720574         0.19647116         0.20367723       -0.143437960        0.203937367        0.294431435        0.184358331        0.272106482        0.260812933         0.29031258         0.18633750       -0.058307777
LU_TUMOR_VASCULATURE_UP                                 -0.303485092         0.05954910        -0.08947968         0.17393748        0.055216604        -0.21711694       -0.068811743        -0.36596763        -0.10701941        -0.26356696        0.360410658        -0.07864957       -0.121613155        0.177822010        -0.01104916        0.229093881        -0.18613941        -0.27316309         0.12995187         0.27171808        -0.30894560        0.172438331        -0.30343314         0.37190436        0.180795286       -0.104016386        -0.07390340         0.21484484       -0.372653361        0.272063159        0.146426458        0.292726824        0.073215278        0.236064108         0.12233488         0.30677400       -0.166297976
KORKOLA_EMBRYONAL_CARCINOMA_UP                          -0.237891606         0.22324873         0.36244453        -0.10961418       -0.136474592        -0.46990350       -0.273764475        -0.16989735        -0.22372057         0.11247316       -0.232337649         0.28697934        0.017986838        0.142356962        -0.07127081        0.189358376         0.18951708         0.36031203        -0.18122486        -0.25323494         0.42996355        0.240702262         0.14655134        -0.29879857       -0.105909705       -0.186176950        -0.23520759         0.11808592        0.123806950       -0.096186587        0.082449346        0.068290275        0.204362056       -0.305158509        -0.18242290         0.07924085        0.050412994
KORKOLA_TERATOMA_UP                                      0.069466630         0.31282751         0.26793152         0.09145777        0.364378105        -0.01610294       -0.429410344        -0.34268743        -0.49321544        -0.29390567       -0.294556431        -0.43171623       -0.275085564       -0.198360712         0.34983219        0.320807082         0.13961117        -0.13440310         0.10165153         0.12248119         0.32044205        0.106653855         0.01837852         0.25031318       -0.310896163        0.053773795         0.03604947         0.33071217        0.066562201        0.280163027        0.039476681       -0.126383734        0.241910733       -0.323470237        -0.03914776         0.30954031        0.103077314
KORKOLA_YOLK_SAC_TUMOR_UP                                0.165072940         0.38624888         0.50530097        -0.37418563        0.006252226        -0.41666427       -0.301013273        -0.13354266        -0.14397323         0.31804861       -0.080548556         0.23290348        0.035345111        0.007931487        -0.09467101       -0.158566311         0.29400647         0.34421179        -0.14156018        -0.16187218         0.22342054        0.257582308        -0.07203685        -0.28296980       -0.390797184       -0.299345198        -0.33442798        -0.05640545       -0.267890012       -0.360997781        0.046532067       -0.038161214        0.260330724       -0.286721001        -0.29560478         0.25567578       -0.058961842
KORKOLA_CHORIOCARCINOMA_UP                              -0.010233903         0.32695285         0.23409239        -0.44995947        0.110491619        -0.77486388       -0.590305245        -0.30294240        -0.37350003         0.22506301       -0.122120864         0.36713585        0.321071992       -0.025352644         0.18055781        0.006019335         0.33689753         0.01559227        -0.39322807        -0.49057169         0.60777944        0.563917133         0.23716208        -0.44914903       -0.257199360        0.181773354        -0.26429369         0.34875870       -0.418331961       -0.402954949        0.279270709       -0.219024970       -0.073131401       -0.377126885        -0.01449304         0.08204518        0.009841082
KORKOLA_SEMINOMA_UP                                     -0.298212257         0.01080115         0.24405821        -0.15938874       -0.027952932        -0.28780633       -0.247319424        -0.33519149         0.06014085         0.22168793        0.058430886         0.28316538       -0.005576346        0.060208089         0.07375198       -0.081445539         0.16610491         0.42430320        -0.01533883         0.08230093         0.24992576        0.077656272        -0.06562014        -0.16684190       -0.284188016       -0.287282092        -0.16462701        -0.05811647       -0.062401658       -0.099243073        0.073201955        0.067154795        0.267030362       -0.298357838         0.02900301         0.32555350        0.080225727
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP        0.097593813        -0.16794685         0.35151193        -0.23237964       -0.163197206        -0.29950843       -0.006714904         0.34062208         0.09604888        -0.11003744       -0.171064434         0.06587775       -0.266062516        0.220122655         0.33608928       -0.127916894         0.11383392         0.19988434         0.20190981        -0.30021326         0.14299295        0.063923084         0.05677644        -0.28986580        0.038510117       -0.159509213        -0.29388778         0.05765373        0.326704138        0.074522409       -0.274247777       -0.275056415        0.053402889       -0.002107284        -0.34859857         0.03644107        0.208732689
HOLLMAN_APOPTOSIS_VIA_CD40_UP                            0.105496299        -0.13988837         0.38579893        -0.24564927       -0.083118397        -0.02283095        0.141139992         0.25611563        -0.05713898         0.01803229       -0.087474542         0.14542629       -0.210191344        0.211687858         0.22093653       -0.133326040         0.06549381         0.18478682        -0.03775017        -0.20148605         0.22321211       -0.059252095         0.01426428        -0.09291203       -0.005412103       -0.025056156        -0.28678304        -0.10392565        0.206300949        0.073580108       -0.204915942       -0.221567934       -0.045463659        0.033396194        -0.24875118         0.01892772        0.157710229
LIU_PROSTATE_CANCER_UP                                  -0.224388256         0.06307335        -0.08241727        -0.04832687        0.189906903        -0.02124567       -0.279030644        -0.27886322        -0.09392327        -0.19792744       -0.029580432        -0.03027978        0.202657103       -0.340883536        -0.03209933       -0.116168855        -0.30287655         0.21450416        -0.04221989        -0.04528200         0.06964423        0.083598831         0.16642355         0.12185052       -0.000928352        0.140595272         0.28592176         0.02379778       -0.071982214        0.154329444        0.077278879        0.239783535        0.316168936        0.045907958         0.11350734         0.06778064       -0.142535169
LIU_SOX4_TARGETS_UP                                      0.121044935        -0.14068822         0.22940559        -0.01597795        0.061591507        -0.00693642        0.014199778         0.30911203        -0.08600822        -0.02038572        0.114287917        -0.21978031       -0.226307014       -0.023607467         0.29166627        0.064022632         0.06822989        -0.07130524         0.23335358         0.06981417        -0.11573705       -0.291602661        -0.13629614        -0.03270145        0.024218801       -0.013336764        -0.10693992        -0.16558042        0.190828338        0.225771717       -0.229823064       -0.164944356       -0.179080910        0.177092706        -0.17646028        -0.18791880        0.240962021
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP            0.062841657        -0.18362789         0.29336781        -0.18594491        0.154299300        -0.05557008       -0.083102532         0.04576576        -0.09217560        -0.19543518        0.055196463        -0.04809592       -0.052719541        0.107250567         0.17234102        0.220352187        -0.04953385         0.24873127         0.13828440         0.19314948         0.04975678        0.049538498        -0.06477196        -0.06226135       -0.098276136       -0.129915554        -0.19707557         0.02496088       -0.051271962        0.052870430       -0.073226448       -0.184972633       -0.012686096       -0.071808834        -0.27150226         0.27912570       -0.135303937
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP                -0.094846112        -0.07207493        -0.02804641         0.03696695       -0.086436392        -0.08397341       -0.068172639        -0.05763452        -0.02656466        -0.17775526        0.258308865        -0.14822566       -0.145150486       -0.039994112         0.10916677       -0.090893212         0.03680901        -0.09371656         0.11806513         0.17785724        -0.11045327       -0.058180594        -0.31826977         0.09626481        0.143735941       -0.160260444        -0.06107374         0.08258827        0.034945942        0.261716811        0.008073164       -0.089058343        0.056294586        0.251527056         0.01348282         0.28709952        0.102083930
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP                 0.074340051         0.02857125        -0.24003150         0.30715667       -0.010403308        -0.10045962       -0.159844495        -0.22324560         0.02880624         0.11715699        0.077777052        -0.17990167        0.106011986       -0.179976522        -0.09660455        0.026469354        -0.12555729        -0.17002077         0.19363609         0.07413777        -0.34472957        0.071120620        -0.23684660         0.25225819        0.214521242       -0.165874245        -0.03452474        -0.02439650       -0.180590309        0.011098030        0.114305528        0.052961087       -0.068405608        0.293293442         0.24643595         0.09297256       -0.030979738
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP                     0.005014724         0.08111308         0.26913235        -0.09552045       -0.450228901        -0.20835559       -0.341832089         0.08934729        -0.33423215        -0.07570491       -0.227456658        -0.31425832       -0.075046342        0.101225498        -0.22803411        0.359148102         0.25779762        -0.50524646         0.12655983        -0.08326589         0.16277302       -0.238058161        -0.17065282         0.06861909        0.125783171       -0.153453577        -0.06888951         0.35891268        0.238976848        0.449575492       -0.397721447        0.129949315        0.063354595        0.344276854         0.21919705        -0.02084416        0.446602851
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP                     -0.086490808         0.42662285        -0.06186335         0.19254225       -0.147417154         0.23175825        0.491914629        -0.11696009         0.01145265        -0.18617542       -0.098643515        -0.08071038       -0.040838732       -0.284554435         0.44402053       -0.167965862        -0.06796364        -0.12183172         0.37256760         0.34632681         0.01477953        0.154501865        -0.14155636        -0.17148626        0.040841265       -0.199318164        -0.03141871        -0.02556187       -0.194745034        0.111576773        0.299019277       -0.246935585       -0.304924920        0.249744542         0.16874813        -0.28320150       -0.409684665
FRASOR_TAMOXIFEN_RESPONSE_UP                             0.095102205         0.13613061         0.27963248         0.10696680       -0.201251938         0.04440738        0.039666191         0.08072985        -0.30347286        -0.13117213       -0.163829152        -0.08811162        0.130289925       -0.269491251         0.04481561       -0.129982372        -0.09261704         0.05779261         0.20931794        -0.11293941        -0.08782228       -0.154603301        -0.10942582         0.03255269        0.068908002       -0.134879788        -0.11865894         0.03929191        0.105215621        0.144775760       -0.132818191       -0.126161041        0.046198277        0.066790819         0.10784581         0.14897625        0.103889267
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP                   -0.093263740         0.24451532        -0.30875436        -0.01171828       -0.077592391         0.06977365       -0.047698353        -0.25543630        -0.16734657        -0.29943342        0.138659259        -0.24677548        0.008316094       -0.097198227        -0.07991562        0.237943766        -0.08176618        -0.34607119         0.18984664         0.28121888        -0.29765020        0.006609358        -0.17838613         0.18555511        0.093828022       -0.218609231         0.17434097         0.06804717       -0.095062879        0.199580074        0.321860622       -0.008284166       -0.001916854        0.183088620         0.25305607         0.13585610        0.034581179
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP                     0.203957767         0.12189117         0.38492132        -0.24300464       -0.090523098        -0.19966713        0.102728363         0.04976671         0.18283638         0.30437400        0.148109727         0.24724848       -0.327248458        0.129670458         0.33143975       -0.086102559         0.10335793         0.20068518         0.03773511        -0.23454620         0.13617294       -0.090673447        -0.26073243        -0.38875239       -0.054723088       -0.050551494        -0.23180710        -0.12601589       -0.001883262       -0.007476349        0.072573918        0.189048383        0.090254301        0.187420576        -0.31338258        -0.10912037       -0.247410905
WATANABE_COLON_CANCER_MSI_VS_MSS_UP                     -0.156524705        -0.00167507        -0.10689295         0.36427412       -0.010218876        -0.06496857       -0.269749963        -0.27745767         0.02119152        -0.21830558       -0.196574719        -0.35120814        0.269162954       -0.142483756        -0.26808257        0.038724466        -0.07004319        -0.11588327        -0.10292213        -0.06427425         0.25284346        0.283925446         0.01040659         0.32549432        0.230151042        0.409316724         0.37175290        -0.27673142       -0.066751401       -0.078279396        0.099369827       -0.165196141        0.013360644        0.168730310         0.23632001        -0.18337713       -0.329485400
> 

GSVA.Rcheck/tests/test_plage_newapi.Rout


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> 
> ## 2023-11-10  axel: simple test script for method PLAGE, new API
> 
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db


> library(GSVA)
> 
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
> 
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
> 
> p <- 10000 ## number of genes
> n <- 30    ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+             dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
           s1         s2          s3         s4          s5
g1  1.4171739 -1.3444519 -0.99052898  0.4203395  1.30716224
g2 -0.7281951  0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754  0.09779699 -0.6792548 -0.09124045
g4  1.0735382  1.3156255  0.15588330 -1.8079608  0.48531108
g5  0.7229884 -0.9162342  1.93982245  0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+                    paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> plagePar <- plageParam(X, gs)
> plage.es <- gsva(plagePar, verbose=FALSE)
> dim(plage.es)
[1] 100  30
> plage.es[seq.int(min(nRowsToPrint, nrow(plage.es))),]
               s1           s2            s3            s4          s5           s6           s7           s8          s9          s10         s11           s12         s13         s14         s15          s16         s17           s18           s19          s20         s21          s22          s23          s24          s25          s26         s27         s28          s29         s30
gs1  -0.029219588  0.134185958  0.3713074711  0.0407816079  0.06092767 -0.220481051 -0.263761945  0.150320487 -0.22409656  0.009584613 -0.39111762 -0.1302648585 -0.05959038  0.33696215 -0.07282788  0.073310843  0.05147115 -0.2483084427 -0.0858324287  0.178309261  0.38540679  0.046642663  0.122541902  0.015905580 -0.097924551  0.029203351 -0.06630956 -0.07126728 -0.194205126  0.14834577
gs2   0.009713309 -0.070894760  0.0887748898  0.0438945086  0.07597568 -0.099232840  0.257432656 -0.180783042 -0.26082831 -0.191077787  0.03035706 -0.1035337259 -0.19412605 -0.10714563  0.07146483  0.086637398  0.20308822  0.0140285507 -0.2137568863  0.239387383 -0.22371195 -0.206819710 -0.133382606  0.108114986 -0.046079067  0.089875594  0.42299690  0.41937892  0.096947556 -0.22669608
gs3  -0.139922266 -0.117741577 -0.0781834024 -0.2165908186  0.27378251  0.311048702  0.086846172  0.044475856 -0.08203218  0.119527132  0.03846745 -0.2109524281  0.12655940 -0.38507377  0.10369939 -0.017494211  0.16994906 -0.1420728947 -0.0785235706  0.004983979 -0.08761015  0.009889028 -0.094132008 -0.247835746  0.083711263 -0.250047995 -0.11800166  0.26164152  0.264615361  0.36701785
gs4   0.136784356 -0.055804012 -0.0003340026 -0.1516269802 -0.27114196 -0.083083560 -0.096565517  0.036868895 -0.06300502 -0.221561203 -0.19813522  0.1042473505  0.08093850  0.05674063 -0.19895817  0.067302708  0.25451893 -0.0005207089 -0.1159880895  0.048467793 -0.20603836  0.159545022  0.044036214  0.534771648  0.105886354 -0.017032347  0.07891909 -0.39111885  0.312125306  0.04976120
gs5   0.034934164  0.039749845  0.1228855856 -0.2732261283  0.04199286  0.103214014 -0.195436449 -0.287379571  0.03966687  0.303622722  0.07474143  0.0856083346  0.13595773 -0.01383837  0.35831980 -0.051209828 -0.43727399  0.1718981370 -0.1181945240  0.089941405  0.27917773  0.023292236  0.118740362 -0.297527028 -0.070561479 -0.048431187  0.02429263 -0.23305662  0.114527349 -0.13642802
gs6  -0.279844320  0.191897986 -0.3053996126  0.0094415284  0.04842640  0.194020478  0.096966418 -0.068898812 -0.20073135  0.378243740 -0.19309702 -0.1466213408 -0.14129713 -0.26167877  0.16969940  0.003873402 -0.06359659  0.1923023239 -0.2857295678 -0.037571361 -0.13741602  0.028278539  0.238658744 -0.074846882  0.198735207  0.142033651  0.30737897 -0.09691484  0.003752428  0.08993441
gs7   0.225539026  0.254315627  0.0211474628  0.3655580391  0.12888554  0.040475802 -0.108671963 -0.177723642  0.41116878  0.227671549 -0.28572797 -0.0471024585 -0.11298848 -0.14563561 -0.04101156  0.001529252 -0.30955146  0.2015628322 -0.0515248852 -0.202779772  0.26345240 -0.037525716 -0.006683093  0.089664221 -0.112755956 -0.152690537 -0.11819571 -0.06373540 -0.095213785 -0.16145252
gs8  -0.231283677 -0.053675557  0.0264131810  0.1359540470  0.08233788 -0.227928562 -0.087182432 -0.090687865 -0.08943693  0.307308887 -0.26623882  0.0138228392  0.21217554 -0.01320852 -0.37951349 -0.052096781  0.10783552  0.1598299126 -0.2189896514 -0.112309675  0.24977969 -0.065970466  0.140396761  0.076196677 -0.330320943  0.135782120  0.26952133  0.29550850 -0.055760954  0.06174143
gs9  -0.149696707  0.070112664 -0.3927757978  0.0404540759  0.05022070  0.286507502 -0.292734447 -0.111830390  0.01797344 -0.123194982 -0.12329977 -0.0405767884  0.05003308  0.38368419  0.01421485  0.062677869 -0.07909931  0.0486677864  0.0095880253  0.132223596 -0.28737944  0.178169340 -0.379773116  0.242912453  0.188194766  0.217203390  0.11001738 -0.02903181 -0.001529958 -0.09193259
gs10 -0.117672007  0.025542827  0.1308302520 -0.1626636222 -0.09699436  0.244461645  0.359249078 -0.191834856  0.03983472  0.146795086  0.06267437 -0.0434347372 -0.04176742 -0.06732570  0.13904093 -0.305077580 -0.02187673  0.1570480436  0.1334628532 -0.279021420  0.06938138  0.363531649 -0.201888466  0.258009015  0.084167939 -0.202884988  0.12079417 -0.11859744 -0.252643549 -0.23114107
gs11 -0.117405216 -0.048550062 -0.2152359244  0.1765495035 -0.15055137 -0.123720213  0.102298045 -0.027754231  0.20009873  0.250537460 -0.05653296  0.5188172981 -0.14533038  0.18956907 -0.05111332 -0.028603358 -0.08113559 -0.1326973408 -0.2163548884  0.153306782 -0.24927555  0.377259651 -0.143092985 -0.138807673 -0.201352437 -0.049677679 -0.09122352  0.11203847  0.069118818  0.11882086
gs12 -0.543671749 -0.184614928  0.1099977497 -0.0553393639 -0.40340420  0.033822756  0.082140727  0.090566044  0.06267315 -0.035981570  0.18191246 -0.1165185323 -0.14432586  0.18146646  0.03547440  0.236193030  0.02238259  0.0383756956 -0.0935119488  0.043760861  0.02041612  0.063399434  0.120073412  0.080158878 -0.122419354  0.011193111  0.21268970 -0.20265505 -0.123185463  0.39893143
gs13 -0.024887916  0.118584422  0.1388041889 -0.1413124768 -0.39825505  0.052045207  0.261267389 -0.255779352  0.08983137  0.244926313  0.25970077 -0.0188348892 -0.36760612 -0.01271960 -0.20002981 -0.087057056 -0.05944590 -0.1591285151  0.2077404356  0.302011283 -0.02371886  0.178685780  0.016103242 -0.065410956  0.141870716 -0.181431006  0.21774895 -0.11979818  0.016494216 -0.13039859
gs14 -0.100340055  0.077189402  0.0390858762 -0.0370017538 -0.38389060  0.184412799 -0.118805404  0.151984291 -0.25219352 -0.107177720 -0.13513101  0.0625168832 -0.10590181 -0.17815359  0.03224044  0.159411109 -0.08896745 -0.1280661493  0.1577303651 -0.038406698 -0.27702921 -0.122279723  0.239019808  0.128024840  0.212749941  0.142712690  0.18985273 -0.29773955  0.378010038  0.21614304
gs15  0.048774560  0.060119682  0.0484913743  0.2519843778  0.03039694 -0.234375681 -0.108291508 -0.453456336  0.06303550  0.086507823 -0.04349266  0.0260079589 -0.07031311 -0.07260948  0.19503960  0.264057607  0.30593891  0.1027550963  0.2715334959 -0.065807601 -0.15451764  0.253065015 -0.142033610  0.149114814 -0.156868088 -0.142545833 -0.28141243 -0.15529889  0.134277793 -0.21007769
gs16 -0.121838108  0.078038618  0.1774058118  0.3701311334 -0.27325953  0.179212470 -0.183228978 -0.297884469  0.07431105  0.142904264 -0.37912167  0.0392912596  0.31140398 -0.15567324  0.30015891 -0.075661103 -0.09261959  0.0039456916 -0.0540112724 -0.046884108  0.18371220 -0.073575237  0.236113549  0.114082325 -0.059486224 -0.043877650  0.05583114 -0.19847973 -0.131850692 -0.07909080
gs17  0.184799857  0.070052354  0.3514429664  0.1732326612 -0.22022967  0.003214861 -0.405239687 -0.047291743 -0.24679440  0.160056459  0.08518827 -0.0463285866 -0.06034854 -0.30001767 -0.19348991 -0.035213712 -0.09465668  0.0759894988  0.1785756235 -0.132155045 -0.17500659  0.376832927  0.013218793  0.018574170 -0.110793912  0.229997712  0.16584921  0.05705518 -0.156772307  0.08025791
gs18 -0.187087483  0.337139118  0.1688542303  0.1173035568  0.05984658 -0.185941480 -0.119363637 -0.382728482 -0.15395065 -0.319451357 -0.19733920 -0.0144161899  0.24873343 -0.10552473  0.04524322 -0.001873581  0.22373606  0.0229936448 -0.3542996024  0.061859205  0.02839072  0.078164766  0.344304336  0.045874812  0.009125945  0.025623338  0.17909395  0.09353534 -0.131011234  0.06316538
gs19 -0.059003209 -0.199168662 -0.1837419847 -0.2237610050  0.39738058 -0.326919064  0.087628623  0.181877873  0.35191549 -0.027680315  0.24795143 -0.1101431952 -0.01839169 -0.16235495  0.08701808 -0.090546490  0.16014091  0.1263778250 -0.0780805378  0.230737817 -0.22144812 -0.217901043 -0.019311240 -0.228211869  0.086283799 -0.067073673  0.17863523 -0.10809469  0.095046484  0.11083758
gs20 -0.087459182 -0.195412041 -0.0130357705  0.2848639974  0.22802341 -0.158851672 -0.203819293 -0.074651734  0.26441584 -0.163246538 -0.16645128 -0.0007860099  0.23034725 -0.10381161 -0.44439333  0.400370645  0.17176277  0.0072304296 -0.0820074325  0.083326015 -0.18145094 -0.041971647  0.076837721  0.000302442  0.174386727 -0.151895543 -0.01190509  0.10267278 -0.134531574  0.19114066
gs21  0.107602195 -0.142208461 -0.1560412602  0.1057618700  0.08242831 -0.094411152 -0.402862002 -0.372859070  0.03195170 -0.056225322  0.02369290 -0.0133280573 -0.19355100 -0.27795918 -0.03191200  0.364990768  0.28739587  0.1564537944  0.0719681085  0.169215470  0.29072561 -0.251367594  0.063227672  0.159273607 -0.096533492  0.163138228  0.01013211 -0.06972215  0.049191913  0.02183063
gs22  0.281156732 -0.185969190  0.1466983344  0.0988277638 -0.05639434  0.008345487  0.314359229 -0.035846835 -0.02674254  0.048462980  0.04194433 -0.2929134701 -0.02180503  0.16130641 -0.09628426  0.094556572 -0.17393215 -0.0501843811  0.0418822082 -0.042590804  0.17563655 -0.241418448  0.454068984 -0.195659705 -0.078786970 -0.020000914 -0.31312338  0.24019694  0.013901423 -0.28969152
gs23  0.287000160 -0.009577127 -0.0258026809  0.3978394227  0.06574872  0.165351593  0.202895394 -0.008028034 -0.07998444  0.210698794  0.07377611 -0.0586860376 -0.15454336  0.13418397  0.08296051 -0.055745695 -0.06072953  0.0004303990 -0.0731050722 -0.109362156  0.03413574 -0.043312239 -0.067080708 -0.310656179 -0.124265593 -0.262454623 -0.54504850  0.22851199  0.123089583 -0.01824042
gs24  0.226216800 -0.073685267 -0.0417664264 -0.0006964549  0.18170065  0.466969874  0.008804967 -0.038827882  0.15703216 -0.158480858 -0.21933991 -0.0418454781  0.08244118  0.05264244  0.19388981  0.261405034 -0.08604337 -0.2537728142  0.0002742249  0.022868190 -0.15317303 -0.197659709  0.102648478  0.127786731 -0.008318546 -0.272121666  0.17408086  0.09227398 -0.213205479 -0.39209848
gs25 -0.227611755  0.023775737  0.0723240408 -0.1495365735  0.06081540 -0.172945821 -0.104641914 -0.283228744  0.09443370  0.264032568 -0.30609675  0.1905985693 -0.15253022  0.33940139  0.05489225  0.083252511  0.19734533 -0.0236399481  0.2777489932  0.036835483  0.17108518 -0.190520756  0.150268031 -0.160683713  0.167731621 -0.006525896  0.10202510  0.02616628 -0.376857271 -0.15791283
> 
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+                     featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+                     sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+                                       grep("^REACTOME", names(c2BroadSets)),
+                                       grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- plageParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+                       minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
                                                    NA19099     NA18523     NA19144     NA19137     NA18861     NA19116      NA19130     NA19131     NA19119     NA19152      NA19153      NA19140      NA19138      NA18522      NA19192      NA19193      NA19239      NA19238      NA19210     NA19201     NA19172      NA18870     NA18858     NA18852     NA19159     NA18855     NA19204     NA18501     NA19127      NA19098       NA19093      NA18856      NA18912       NA18517     NA18502       NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                  0.11442430  0.32079541  0.19023827 -0.16386259 -0.34124516 -0.08626990  0.006244354 -0.09133096 -0.07958067 -0.19080877 -0.129759539 -0.011392352 -0.053528324  0.137113192  0.122790549  0.185113826  0.255475291  0.289729331 -0.231805083 -0.10599439 -0.16563165  0.254730153  0.28736502 -0.07380857 -0.13262739 -0.00202695 -0.12848634  0.04738066  0.15451669 -0.042949836 -0.1917455098 -0.158789670 -0.030545427  0.1681240794 -0.02372029 -0.0981317670
KEGG_CITRATE_CYCLE_TCA_CYCLE                    -0.14376128 -0.40210177 -0.10732752  0.22556600  0.22044109 -0.04149364  0.082632466 -0.03088703 -0.10141600  0.21634351 -0.099937129 -0.238283100  0.059799913 -0.044056815  0.106146035  0.035855219  0.056963046 -0.091694988 -0.111915190  0.08270476  0.17136294  0.002778763 -0.17116078  0.04310892  0.38606731  0.26041385  0.18985748 -0.28660545 -0.22184771 -0.072806417  0.0353622058  0.097891536 -0.169106885  0.1413099205 -0.11591220  0.0357089449
KEGG_PENTOSE_PHOSPHATE_PATHWAY                  -0.16235500 -0.32582108 -0.11076423  0.23827639  0.33496725  0.02867445  0.017174780  0.06591909  0.10482653  0.18448109  0.051993550 -0.025185654  0.117266799 -0.086462365 -0.121860074 -0.309601472 -0.202595001 -0.203907440  0.166706699  0.13841854  0.05621760 -0.217255930 -0.23400863  0.03480311  0.03693621  0.18017005  0.17067361 -0.14698325 -0.15401687 -0.039631290  0.1852566211  0.251925461  0.059502652 -0.1710616230 -0.05714658  0.1444660100
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS   -0.19045563 -0.30144436 -0.06208281  0.23907573  0.23514442 -0.11949500  0.256530147 -0.15784897 -0.07002696  0.18754970 -0.156566301 -0.233437891 -0.028875826 -0.135832499  0.007013319 -0.063573306 -0.045190431 -0.134951243 -0.119095747  0.08957830  0.20494217  0.014625096 -0.21685204  0.12579094  0.30068903  0.30284667  0.20017848 -0.22704585 -0.03911287  0.152821859 -0.0118501734  0.195309455 -0.129960080  0.0414442346 -0.05624288 -0.0535986719
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM             0.08708061  0.36924639  0.16317478 -0.18733952 -0.22969884 -0.07403687  0.005513622 -0.13403336 -0.10757766 -0.11347043 -0.126968905 -0.068529526 -0.073097377  0.145409314  0.117559506  0.192280283  0.262745324  0.261030448 -0.187064190 -0.10806619 -0.21446933  0.264815017  0.32316348 -0.02316450 -0.08242710  0.09121413 -0.08115837 -0.06082489  0.05128248 -0.096144492 -0.1729482337 -0.179767986  0.079378632  0.2025544282 -0.14107384 -0.1545868541
KEGG_GALACTOSE_METABOLISM                        0.13896759  0.33236986  0.15287628 -0.19570500 -0.37392490  0.03112239 -0.101122302 -0.02357435  0.03161318 -0.18551649  0.042859194  0.003683625  0.058836073  0.058593014  0.103013057  0.136717007  0.125649307  0.257519495 -0.059380958 -0.09369887 -0.16262023  0.145102780  0.38948984 -0.18103028 -0.24299641 -0.04474028 -0.20609816  0.05089387  0.23425714 -0.067198742 -0.1327201321 -0.208840024 -0.007338931  0.1015346567  0.02976531 -0.1383576213
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM           0.08699846  0.02769904  0.03088309 -0.15783874 -0.16132270  0.07393045 -0.152562581  0.17928005  0.15457917 -0.11563182  0.248868576  0.203636007  0.038899707  0.177895808 -0.087598070  0.024330837 -0.068874923  0.166621148  0.195566178 -0.09919733 -0.51840256 -0.125338656  0.15816739 -0.06627634 -0.24722350 -0.12644374 -0.27029081  0.23656458  0.03682528 -0.172195675  0.1255991760  0.010036282  0.146200884 -0.1183297380  0.06921028  0.0957347869
KEGG_FATTY_ACID_METABOLISM                       0.25246920  0.21487789  0.06756412 -0.24015561 -0.15971798  0.04164973 -0.134634522  0.18133621  0.18742246 -0.09879733  0.059789040  0.211657105 -0.189741758  0.051073442 -0.063493728 -0.055876110 -0.064518498  0.032865183  0.144745872 -0.12747677 -0.34740988  0.017286592  0.07659859 -0.12250954 -0.14145045 -0.32332540 -0.30311340  0.30156896  0.14235300 -0.020396100  0.1491018982 -0.054180990  0.209632783 -0.0622606872  0.15856855  0.0084981268
KEGG_STEROID_BIOSYNTHESIS                       -0.26848204 -0.15151075  0.27196342  0.20005723  0.05633948  0.06709033 -0.076856972 -0.08144521 -0.11182014  0.23060319  0.031572540 -0.043182612  0.162334518 -0.113794316 -0.221396081  0.039299968  0.198596097 -0.125931968 -0.101950870  0.12788728  0.03906626  0.135077658 -0.01696710  0.13279903 -0.12493729  0.40294067  0.30898303 -0.07471426 -0.07229951 -0.346954681 -0.0425758777 -0.008173547 -0.157861540 -0.0398692105 -0.24333940  0.0194526802
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS              0.22788265  0.27727244  0.12605512 -0.15231262 -0.07420505  0.10099690 -0.110400990  0.02784962  0.28647176 -0.07980438  0.173249992  0.174422862 -0.001563672 -0.107332599 -0.175605638 -0.211736911 -0.291012627  0.054097637  0.082675881 -0.19222910 -0.13208641  0.074845949  0.13658238 -0.04373454 -0.29216427 -0.25438809 -0.14526442  0.35661858  0.13638691  0.113474381 -0.0882569668 -0.027551600  0.137701542 -0.1643334547  0.08505740 -0.0276586587
KEGG_STEROID_HORMONE_BIOSYNTHESIS                0.22975311 -0.04610095  0.10063919  0.12299358  0.03877036  0.13465162  0.088715672  0.03494038  0.14951930 -0.05843410 -0.117297356  0.306369502  0.111144794 -0.204491028 -0.060894682 -0.033714074 -0.112850883  0.124922513 -0.016199947 -0.31755512 -0.07037955 -0.124619972  0.26355333 -0.17914396 -0.22832643 -0.07349334 -0.47727891  0.09134310  0.19265056  0.233158643 -0.0247334479  0.032853743  0.146944492 -0.1899024173 -0.01884571 -0.0486620136
KEGG_OXIDATIVE_PHOSPHORYLATION                   0.04757384  0.42969714  0.09223380 -0.31361918 -0.22482181  0.17872708 -0.156175716  0.03456549  0.07932693 -0.18222063  0.263950703  0.156720262 -0.054368092  0.125986316  0.006787002 -0.084583991 -0.046388261  0.156195922  0.171548956 -0.20861678 -0.19200932 -0.036138327  0.17882865 -0.06323935 -0.25938295 -0.15467774 -0.19415965  0.14534418  0.07217123 -0.002104513 -0.0639220237 -0.134737904  0.153885773 -0.0408505217  0.22491981 -0.1064463186
KEGG_PURINE_METABOLISM                           0.20065318  0.29721544  0.19035916 -0.18768395 -0.14876802  0.07499662 -0.111130384  0.04279520  0.10058079 -0.18253753  0.104394237  0.237489023 -0.156272735  0.004695238 -0.018444109  0.010848786 -0.031681573  0.100509407  0.200116332 -0.20128343 -0.13295068  0.008116163  0.13517872 -0.16149991 -0.22650307 -0.34997849 -0.25612139  0.34931922  0.23373805  0.081067825  0.0055786780 -0.137452124  0.043582088 -0.1302252071  0.06943792 -0.0581394776
KEGG_PYRIMIDINE_METABOLISM                       0.21386387  0.31876668  0.13823771 -0.14977881 -0.22350466  0.05640788 -0.109066678  0.08462733  0.05200829 -0.09300310  0.030350113  0.314550177 -0.257314444  0.018989332  0.005829506  0.037731104  0.070314765  0.162687671  0.059216742 -0.19130213 -0.19705259  0.038453179  0.10999248 -0.11951467 -0.20321833 -0.33534029 -0.21755611  0.34102133  0.23875776  0.060935006 -0.0074629043 -0.180715242  0.033546687 -0.0939514779  0.01458195 -0.0220880991
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM -0.20681031 -0.37748716 -0.12565805  0.26798513  0.26914186 -0.12685519  0.153416637 -0.01650182 -0.14404837  0.28618661 -0.253033160 -0.185735835  0.033980001 -0.059404347 -0.042798179  0.052827743  0.087918043 -0.047097005  0.002603537  0.12045456  0.02098204 -0.038730195 -0.18413718  0.08243411  0.13850374  0.35054894  0.23717572 -0.12482694 -0.12337093 -0.048174199  0.0483989160  0.232747019 -0.087796534  0.0098209646 -0.20356325  0.0009030612
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM     0.01555983  0.39948710  0.26524975 -0.11344673 -0.30536311  0.13871948 -0.119877999  0.01826166  0.03199101 -0.13884023  0.000402732  0.228057870 -0.065492316  0.046027102 -0.120910813 -0.112044381  0.107682776  0.280525919  0.062717644 -0.08761679 -0.31120689  0.045531608  0.16292802 -0.12689384 -0.31176258 -0.11566649 -0.04943121  0.14634414  0.17297063 -0.064286408 -0.1019910400 -0.192809929  0.239116210  0.0222125604 -0.07591641  0.0297711570
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM          0.14011533  0.44950137  0.13715860 -0.21286365 -0.25951992  0.03554671 -0.035671613 -0.01235037  0.10835898 -0.19692749  0.119707919  0.229911107 -0.124986706  0.071248763 -0.050382477  0.112207174 -0.038781286  0.141432934  0.158050492 -0.24246930 -0.20193494  0.019331667  0.10357964 -0.11758175 -0.13149796 -0.30066366 -0.23406437  0.28585381  0.13769399  0.074084706  0.0009278377 -0.149035605  0.067135796 -0.0470514419  0.08543382 -0.1214980980
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION   0.18341492  0.34228948  0.05029107 -0.34818659 -0.10685182  0.09265336 -0.088466493  0.11016160  0.15517234 -0.26698602  0.224420582  0.146464701 -0.044408678  0.093719606  0.048431770 -0.038893096 -0.147876699 -0.001782784  0.121902396 -0.03997209 -0.15444379 -0.033776069 -0.00457758 -0.03957663 -0.17241854 -0.33220603 -0.31794663  0.27603631  0.13609807  0.092390238  0.0150196645 -0.116601679  0.108012207 -0.1542070774  0.21229246  0.0004075145
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS -0.14556385 -0.10361716  0.22024326  0.31503617  0.06126010 -0.11154855  0.086414704  0.09990315 -0.15911865  0.25419971 -0.371443880  0.088126533 -0.008249792 -0.058022569 -0.290894975 -0.038124927  0.289981591  0.243192257 -0.230345230 -0.15276445 -0.12892010  0.072417276 -0.01986629  0.04301764 -0.08484861  0.12551261  0.03154033 -0.09408278 -0.02997378 -0.054032625  0.0911418987  0.151438348  0.140147297  0.0839960430 -0.34942241  0.0332716988
KEGG_LYSINE_DEGRADATION                         -0.27646705 -0.27151298 -0.14559260  0.23343969  0.37761951 -0.14982544  0.071650219 -0.03606215 -0.11370614  0.13919560 -0.059279394 -0.148559519 -0.055897641 -0.004205009 -0.084549331 -0.125562528 -0.038538048 -0.095318136 -0.053812331  0.06965729  0.21281299  0.081810273 -0.18178297  0.22842373  0.26345436  0.22182994  0.31463356 -0.21013663 -0.18109835 -0.054938949  0.0360631509  0.177937829 -0.061732716  0.0873730291 -0.14374132 -0.0235819496
KEGG_ARGININE_AND_PROLINE_METABOLISM            -0.16123111 -0.13057226 -0.11107844  0.02273494  0.21356398 -0.07436990  0.084384101 -0.16407155 -0.25289315  0.14391482  0.036172848 -0.326582857  0.055461961  0.147752762  0.096612753 -0.119843646 -0.098278801 -0.122948974 -0.211625005  0.19972609  0.33443209  0.139927393 -0.24553021  0.20165627  0.28074920  0.22470401  0.20124083 -0.21576039 -0.19741636 -0.022915154 -0.0511405637  0.032249241 -0.025522833  0.1225511902 -0.02111686  0.0150635951
KEGG_HISTIDINE_METABOLISM                       -0.38691525 -0.08953562 -0.10044464 -0.01426187  0.01496539 -0.13622135  0.073354885 -0.08532239 -0.06721292 -0.02768174  0.076490066 -0.047484587  0.166533226  0.046557442  0.088751653  0.005292349 -0.081057843  0.067987559 -0.094320047  0.21609906  0.44120825 -0.100792083  0.13452155  0.08461381 -0.02486270  0.31367516  0.26079310 -0.32426284  0.10030542 -0.211640562 -0.0433522226  0.176759090 -0.192709853  0.0459120461 -0.22119461 -0.0645469418
KEGG_TYROSINE_METABOLISM                        -0.32712829 -0.42822607 -0.12167600  0.02926148  0.09223972 -0.04442842  0.021231012  0.02765216 -0.03822786  0.04965165  0.123045871 -0.128743087  0.217063631 -0.020137764 -0.074664972 -0.110309150  0.009697748 -0.014759694 -0.068874216  0.21673625  0.25233361 -0.119479733 -0.10033969  0.17709985  0.13429743  0.33966951  0.19420105 -0.33874057 -0.09490785 -0.124655343  0.1026505643  0.260903234 -0.098142875  0.0001200643 -0.07224524  0.0778319820
KEGG_PHENYLALANINE_METABOLISM                    0.40967474  0.19836523  0.08736858  0.02869842 -0.01374240 -0.09317232  0.234731915 -0.10208931 -0.02436911 -0.04192146  0.046894702 -0.010923766  0.047580560  0.042336433  0.092609398 -0.004019050 -0.309686433 -0.136083760  0.434626863 -0.10463787 -0.38590280 -0.094165597  0.21855328 -0.17952300 -0.11488955 -0.05718921 -0.22158783 -0.01384747  0.01198482 -0.007884161 -0.0977790774  0.182631715  0.047187141  0.0992475649 -0.03286374 -0.1362134528
KEGG_TRYPTOPHAN_METABOLISM                       0.15935872  0.31858549  0.09156412 -0.23847420 -0.09302019  0.08275092 -0.025728297  0.07322292  0.19026430 -0.13868036  0.206619445  0.128988091 -0.078007790  0.096592856  0.011962634 -0.051351485 -0.180762468  0.061269834  0.238903090 -0.09208227 -0.10207168 -0.106243834  0.06774698 -0.08751554 -0.26540552 -0.25036631 -0.51241085  0.26365030  0.06499509  0.024424527  0.0203047444 -0.027556007  0.180543189 -0.0780303726  0.07999529 -0.0340353504
> pickrellPar <- plageParam(pickrellCountsArgonneCQNcommon_eset,
+                          canonicalC2BroadSets, minSize=5, maxSize=500)
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esrnaseq[seq.int(min(nRowsToPrint, nrow(esrnaseq))),])
                                                    NA19099     NA18523       NA19144     NA19137     NA18861     NA19116     NA19130     NA19131    NA19119     NA19152     NA19153       NA19140       NA19138     NA18522       NA19192    NA19193       NA19239       NA19238       NA19210      NA19201     NA19172     NA18870       NA18858     NA18852     NA19159     NA18855     NA19204    NA18501     NA19127      NA19098    NA19093     NA18856     NA18912    NA18517      NA18502       NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                 -0.15214812  0.19079795  0.0106548721 -0.06539635 -0.11195287 -0.04362555 -0.31151529 -0.07757363  0.4492669 -0.18037776  0.04612305 -0.0300515212  0.0095461535 -0.17685565  0.0346814651  0.2305611 -0.0811595896  2.228039e-02 -0.0263523574 -0.003290343 -0.17154720  0.13948803  0.0247698576  0.13773137  0.13227548  0.14302214 -0.11441695  0.3020346  0.07079582 -0.052860583 -0.4212291  0.15020276  0.16979426 -0.1934081  0.003119229 -0.0533843888
KEGG_CITRATE_CYCLE_TCA_CYCLE                     0.15203505 -0.17111274  0.0192425535  0.05927134  0.10807196  0.11312140  0.28808722  0.12139802 -0.4880436  0.15299104 -0.04906447 -0.0147576258  0.0316875534  0.11937406  0.0089518864 -0.2637738  0.0406273352 -4.893202e-02  0.0399987391  0.020132090  0.24689245 -0.14284022  0.0008861416 -0.16483674 -0.08846222 -0.14421236  0.18663124 -0.3056940 -0.10053188  0.025582990  0.2761436 -0.11072658 -0.17974086  0.2615204  0.021548560 -0.0214665332
KEGG_PENTOSE_PHOSPHATE_PATHWAY                  -0.15765014  0.18674949 -0.0273930657 -0.07307133 -0.10533768 -0.09164663 -0.32248478 -0.11596237  0.4765833 -0.14616308  0.04285343 -0.0546959513 -0.0078616045 -0.15559699  0.0056289676  0.2402897 -0.0654167765  9.649199e-03 -0.0248954667  0.014836184 -0.19279004  0.15939724  0.0142917986  0.15493177  0.12077530  0.12820289 -0.13375282  0.3157634  0.06478541 -0.032853560 -0.3012578  0.15637181  0.18509625 -0.2567167  0.011332850 -0.0219922268
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS   -0.09948024  0.17081884  0.0007132175  0.03385509 -0.06241216 -0.10503442 -0.20057306 -0.07219669  0.3963326 -0.12678766  0.06517810  0.0224058492  0.0671487290 -0.18608845  0.0013261299  0.2291769 -0.0210756261  2.665083e-02 -0.0991881059 -0.005604071 -0.49238630  0.15844499  0.0684573628  0.18159133  0.06988761  0.19261084 -0.14240752  0.2382392  0.02679420 -0.052668574 -0.3419867  0.13615421  0.10134608 -0.2093921 -0.007625566  0.0377750733
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM             0.11684514 -0.15932375  0.0424584303  0.08863850  0.01606414  0.07687084  0.26942124  0.09040454 -0.4770715  0.19043992 -0.02814712  0.0084783419  0.0113907130  0.11293532  0.0081665138 -0.2110960  0.0520711362  5.324071e-05  0.0002572043  0.004341436  0.20787937 -0.14010382 -0.0237929613 -0.14074488 -0.11101353 -0.11615857  0.13347359 -0.3440427 -0.08201004  0.014824329  0.4008495 -0.13645213 -0.18798271  0.2656192  0.001164264  0.0452927563
KEGG_GALACTOSE_METABOLISM                       -0.10572541  0.20093414 -0.0337689448 -0.06828622 -0.05141289 -0.04603842 -0.27803249 -0.08715881  0.4593304 -0.16948100  0.02158359 -0.0228842754 -0.0251350377 -0.13562816 -0.0336397673  0.2240697 -0.0559377116  3.578987e-02 -0.0187799930 -0.009111103 -0.19168860  0.14544677  0.0582003469  0.14876379  0.04249027  0.08803668 -0.15131539  0.3368992  0.07977192 -0.004153293 -0.4096545  0.16989169  0.19432462 -0.2523470  0.001213619 -0.0565674873
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM          -0.18741437  0.16387617 -0.0060310939 -0.03859070 -0.14802565 -0.06396724 -0.33253815 -0.09961008  0.4362764 -0.27301158  0.09626864  0.0270197462  0.0232057101 -0.31223804  0.0187798020  0.2361106 -0.0726098042 -4.028766e-03 -0.0969205827  0.054098119 -0.09624125  0.17262148  0.0381393930  0.13351280  0.05969382  0.20522582 -0.04629863  0.2630025  0.13133577 -0.077179005 -0.3109268  0.07680757  0.15756403 -0.1319563  0.004626489 -0.0005768344
KEGG_FATTY_ACID_METABOLISM                       0.14404628 -0.17549826 -0.0168733006  0.03662427  0.13805007  0.13510632  0.29212490  0.11769787 -0.4538781  0.16997502 -0.05292794 -0.0171357447  0.0056091986  0.20068593 -0.0171192068 -0.2391582  0.0523800221 -3.355725e-02 -0.0037541309  0.007606301  0.26720390 -0.13680786 -0.0229006319 -0.12955701 -0.16649337 -0.18843753  0.11227260 -0.3030089 -0.07180728  0.065746889  0.3537898 -0.09725041 -0.16000999  0.1584219  0.002131614  0.0267022633
KEGG_STEROID_BIOSYNTHESIS                       -0.23993046  0.13867049  0.1187377626  0.05110320 -0.13720084 -0.17477296 -0.20358441 -0.12237759  0.4362713 -0.01023068  0.09255610  0.0831711016 -0.0316845885 -0.09055792 -0.0101667462  0.2066797  0.0664619590  6.476799e-02  0.0581287322  0.001741120 -0.22245981  0.14966908 -0.0538040397  0.16575480 -0.03806247  0.08839711 -0.09754098  0.3146994  0.09568740 -0.024727977 -0.3582404  0.08721987  0.08303645 -0.3500921 -0.182876427  0.0455568716
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS             -0.10378950  0.13345241  0.0602863571 -0.16623904 -0.07063215  0.01365008 -0.19534754 -0.17435286  0.4708230 -0.07118342  0.11618557 -0.0502633451 -0.0554177755 -0.16614665  0.0076810221  0.2090015  0.0672454536  3.512318e-02 -0.0428960078 -0.024698829 -0.33368337  0.14917398  0.0139906079  0.08658955  0.10773984  0.14806389 -0.11894824  0.3430318 -0.01837218 -0.088410625 -0.4130314  0.11951559  0.13746845 -0.1309977 -0.048676576  0.0540649156
KEGG_STEROID_HORMONE_BIOSYNTHESIS               -0.21197941  0.18630856  0.0301018384 -0.11630509 -0.04474517 -0.08691530 -0.11027761 -0.11733030  0.4409750 -0.20162476  0.13665328  0.0221236331 -0.0003285179 -0.14428211  0.0620844698  0.1180512  0.0562025241  1.740092e-01 -0.0893062456  0.018200638 -0.29453200  0.08782095  0.0795061796  0.14770804 -0.04685136  0.10482351 -0.13782587  0.3286641 -0.01216641  0.001473664 -0.4633424  0.07796440  0.16692838 -0.1512924 -0.030595788  0.0201011702
KEGG_OXIDATIVE_PHOSPHORYLATION                   0.11392670 -0.15176080 -0.0078716193  0.03185503  0.08755261  0.16899727  0.27816007  0.10828366 -0.4984539  0.15443204 -0.05388480 -0.0005382922  0.0143975861  0.13323583 -0.0144179595 -0.1631206 -0.0012127107 -4.539461e-02  0.0435086752  0.022640863  0.29947218 -0.13776551 -0.0302126129 -0.18067891 -0.13765087 -0.16335643  0.12104839 -0.3312689  0.02163840  0.030604155  0.3449082 -0.11292053 -0.11048607  0.2310232 -0.025202957 -0.0394868208
KEGG_PURINE_METABOLISM                           0.14576228 -0.17970119  0.0695643645  0.07390013  0.09426888  0.14811626  0.25313045  0.12971197 -0.4997313  0.16664358 -0.06909949 -0.0011720262 -0.0279803304  0.13994248  0.0019350762 -0.1746847  0.0245422008 -6.364770e-02  0.0941657279  0.013648424  0.26762396 -0.16851615 -0.0456918476 -0.19287243 -0.08967612 -0.14275219  0.16046531 -0.3211839 -0.02696631  0.051340413  0.2707759 -0.12761083 -0.17070100  0.2401788 -0.012335268 -0.0313934410
KEGG_PYRIMIDINE_METABOLISM                      -0.15527782  0.18681216 -0.0710134938 -0.09272258 -0.09107116 -0.15945406 -0.26422713 -0.13051958  0.4924685 -0.17590868  0.06869025  0.0017294883  0.0440173962 -0.15137425 -0.0069782437  0.1818896 -0.0252424604  5.910549e-02 -0.0641390004 -0.009211103 -0.25500824  0.17506163  0.0368705159  0.19122864  0.11892819  0.15054298 -0.17164591  0.3047345  0.02982096 -0.059310144 -0.2438609  0.10353402  0.16710577 -0.2540935  0.041640375  0.0268777463
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM  0.16187518 -0.15242447  0.0445845851  0.03801959  0.16815027  0.15816036  0.18629258  0.13647099 -0.4547896  0.15764760 -0.09834758 -0.0673653703 -0.0327515803  0.13813612 -0.0001154741 -0.2242866 -0.0035237558 -8.144324e-02  0.0846143930  0.016951778  0.35755319 -0.12650621 -0.0869564600 -0.15472376 -0.13565892 -0.15047719  0.19304761 -0.2923463 -0.10340182  0.124156397  0.2929275 -0.08529239 -0.17347808  0.1458381  0.019564617 -0.0001020227
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM     0.18425567 -0.21997777  0.0792549975  0.02796617  0.15066508  0.13108206  0.09096202  0.09603363 -0.4087696  0.19271142 -0.11346497 -0.0412294265 -0.0825276719  0.25407808 -0.0336109990 -0.1920607 -0.0511250493 -1.385250e-01  0.0965515196 -0.005825203  0.28983157 -0.12541010 -0.0631413865 -0.18063408  0.07210946 -0.15207612  0.12502562 -0.3434555 -0.08266163  0.241050135  0.2367705 -0.13650734 -0.16052837  0.1219852  0.122337569  0.0188602175
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM          0.21582742 -0.19257267  0.0481026570  0.12532384  0.12863263  0.12702487  0.21916790  0.14145654 -0.4628510  0.18903573 -0.08990904 -0.0356654022 -0.0293211714  0.21616290  0.0113339421 -0.2359683  0.0240081539 -8.452455e-02  0.0615230196 -0.031731840  0.26949610 -0.14960573 -0.0490440852 -0.18626782 -0.06807870 -0.13588057  0.13260775 -0.3153507 -0.07004173  0.095123437  0.2314867 -0.12190522 -0.17317799  0.1942247  0.001740289 -0.0003819966
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION  -0.13320980  0.19146649  0.0001692046 -0.04724794 -0.11203115 -0.10900765 -0.32384751 -0.08670029  0.4661106 -0.15194445  0.02163166  0.0263972205 -0.0156839833 -0.23372426  0.0016790308  0.2330446 -0.0339518900  2.867854e-02 -0.0347112069 -0.013832614 -0.26086893  0.15508615  0.0463970898  0.12786410  0.13562535  0.16840661 -0.11800503  0.3056234  0.08931534 -0.062290601 -0.3304639  0.11023004  0.15287141 -0.1761863 -0.010338119 -0.0065512747
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS -0.18497233  0.17649821  0.0506236410 -0.08746720 -0.15678895 -0.18326441 -0.19998683 -0.08831954  0.4498416 -0.09855080  0.04904952  0.0387063020  0.0391040897 -0.19473731 -0.0088725559  0.2294151 -0.0153974275  8.110413e-02 -0.0361551097 -0.038686397 -0.29902619  0.15638790  0.0813030069  0.15365219  0.07778971  0.14702327 -0.22562370  0.2961998  0.06095390 -0.060339944 -0.3294075  0.14871582  0.15615268 -0.1661644 -0.018031872 -0.0007282847
KEGG_LYSINE_DEGRADATION                         -0.14840078  0.19887266 -0.0896794806 -0.05874662 -0.09522200 -0.16067588 -0.25024857 -0.12714531  0.5089357 -0.17188541  0.06501566  0.0211715670 -0.0087000106 -0.11468731 -0.0192207645  0.1887464 -0.0086852919  9.220565e-02 -0.0997662839 -0.015545295 -0.25889646  0.14938001  0.0102360429  0.15953226  0.08245914  0.11756512 -0.12447080  0.3428059  0.05803155 -0.041416622 -0.2706288  0.11974209  0.19925355 -0.2252852 -0.018670642 -0.0059757956
KEGG_ARGININE_AND_PROLINE_METABOLISM            -0.15599441  0.17162854 -0.0165755907 -0.04984281 -0.13252570 -0.13503025 -0.24149898 -0.12496608  0.4652361 -0.18264708  0.06245441  0.0533993450  0.0200002688 -0.17588537  0.0187300201  0.2268855 -0.0308582433  6.457058e-02 -0.0409831672 -0.022302704 -0.26703092  0.13286020  0.0597241639  0.15221801  0.12299299  0.13822870 -0.16751098  0.3220956  0.08792924 -0.097087427 -0.3352892  0.08674901  0.18213748 -0.1854224 -0.015128027  0.0087392720
KEGG_HISTIDINE_METABOLISM                       -0.16341627  0.21211137 -0.0597047650 -0.07019812 -0.06569836 -0.16907760 -0.24238369 -0.09397806  0.4720904 -0.22248144  0.09449529  0.0337872241  0.0814929382 -0.14765066  0.0166344423  0.1896539 -0.0151032687  7.080535e-02 -0.0387446192 -0.034208862 -0.28356932  0.13501819  0.0592272252  0.14530433  0.09060491  0.16483382 -0.08830364  0.3105553  0.03130984 -0.076375024 -0.3379780  0.10320490  0.12281655 -0.2312373 -0.020753794  0.0269168631
KEGG_TYROSINE_METABOLISM                        -0.10093863  0.18267763 -0.0242538303 -0.06443060 -0.02632197 -0.16928691 -0.21835995 -0.12802624  0.4897721 -0.20718144  0.08915284  0.0230208339  0.0685731978 -0.11497401  0.0264683523  0.1715784 -0.0240623350  5.461238e-02 -0.0359349395 -0.041186627 -0.34571344  0.11565207  0.0429404806  0.15350966  0.12352853  0.16156040 -0.14241499  0.3437890 -0.02098569 -0.034677062 -0.3320536  0.12420589  0.08212171 -0.1959923 -0.039814920  0.0134459864
KEGG_PHENYLALANINE_METABOLISM                   -0.13596282  0.06742145  0.0882449903 -0.02244406 -0.09867622 -0.06439912 -0.08447981 -0.15306648  0.4203738 -0.10031185  0.17368849  0.0780588540  0.0996577430 -0.02544390  0.0171562407  0.1211227  0.0235791297  8.347408e-02 -0.2466780511 -0.006247915 -0.61710863  0.07252436  0.0317753835  0.10302349  0.06683344  0.11139551 -0.15093291  0.2664307  0.04334024 -0.011422551 -0.1744265  0.11107338  0.02648540 -0.2152238  0.019167613  0.0819975622
KEGG_TRYPTOPHAN_METABOLISM                       0.17049240 -0.19170650  0.0004630847  0.05089247  0.12593277  0.11515466  0.27670376  0.12909756 -0.4814202  0.17977370 -0.06320424 -0.0194461931  0.0070929693  0.19100894 -0.0230060896 -0.2042648 -0.0001048516 -7.878183e-02  0.0931404987 -0.026808640  0.24465868 -0.13838085 -0.0248749524 -0.16243909 -0.09741608 -0.15878157  0.07600539 -0.2897865 -0.09352519  0.056621625  0.3530154 -0.08401918 -0.15938269  0.2105366  0.043211634 -0.0264526019
> 
> gbmPar <- plageParam(gbm_eset, brainTxDbSets)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
                    TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up               0.009503434         -0.07148275          0.03702570          -0.1449671         -0.06040476         -0.07594821         -0.08471232        -0.011938741          0.02993423         0.065023141          0.01762836         -0.11912551         -0.05949992          0.00525537         -0.05523948         -0.05372246         -0.08443369         -0.08598174         -0.11875051        -0.042058976         -0.04030687        -0.085476621         -0.10685594          0.02611153          0.04356317       -0.0705649980        -0.006844708         -0.01728745         -0.05473265         -0.02670516        -0.023271397         0.028072017         -0.03921781         -0.10235048         -0.05010187         -0.07005158         -0.09209016         -0.10881587         -0.05062336        -0.007877207         -0.08243841         -0.06962198         -0.08767648         -0.02583498         -0.04666987         -0.07810986         -0.01152421          0.02981450         -0.08655273        -0.024763415
astroglia_up                0.047878697          0.13259958          0.09353196           0.1723954          0.05397369          0.09437815          0.12333017         0.034441261         -0.02691552         0.082648790          0.05525398          0.07854437          0.02675066          0.14436470          0.03635936          0.07445693          0.18500914          0.12978579          0.10685532        -0.046038185          0.03640657         0.134998687          0.14571431          0.16997016          0.02481540        0.0363660300        -0.020974725          0.08501924          0.13807016          0.11677809        -0.008999474        -0.020349973          0.05204384          0.04461865          0.09432334          0.05564952          0.05441292          0.07187041          0.06496384        -0.016408375          0.06458610          0.08187014          0.14767961         -0.01197801          0.03687600          0.06445718          0.01797752          0.01595298          0.09244863         0.052499964
neuronal_up                -0.109710924         -0.01702066          0.01301810          -0.0150155         -0.09724660          0.02146057          0.05010519        -0.040146081         -0.06066290        -0.006770987         -0.11536936          0.07187279          0.06404673          0.05934842          0.01706701          0.06703005         -0.05028874          0.06844218          0.03520158        -0.007305407         -0.02100709        -0.009551983         -0.02286479          0.02104686          0.02714991        0.0009992218        -0.091286596          0.04988690          0.05224805          0.04092799        -0.012195643         0.009698397         -0.03329177         -0.03730078         -0.06501777          0.00777109         -0.01276343         -0.07101898         -0.03167425         0.008950496         -0.04525475          0.03152291         -0.05007149         -0.06206634          0.00277177          0.05362907          0.06015409         -0.12476908          0.01965553        -0.006541254
oligodendrocytic_up        -0.053316262         -0.03076570         -0.13026183          -0.1054244         -0.15884604         -0.04584733          0.01162552        -0.008735686         -0.07831724         0.029790216         -0.12264757         -0.17633055         -0.22829418         -0.09563053          0.01913198         -0.08062237          0.06710752         -0.04973426         -0.09459566        -0.035043759         -0.07087794        -0.024834220         -0.14132943         -0.08015759         -0.12351419       -0.1018570138        -0.145485987         -0.08031675         -0.13791221         -0.06314112        -0.055013638        -0.111969729         -0.06278656         -0.12395121         -0.11149668         -0.13560637         -0.03100847         -0.11540779         -0.19569986        -0.004032233         -0.09848717         -0.01310448         -0.01601479         -0.08806238         -0.15998008         -0.03256551         -0.02666356         -0.04873438         -0.04271502        -0.015764935
                    TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up               -0.10887523         -0.07864038         -0.04197239         0.095668384          0.18776408          0.25307779          0.08792407          0.05994647          0.13261591         0.021215334           0.1151069          0.12610727          0.11787216          0.03692715          0.07098464          0.06193001          0.05640898          0.07437529          0.03446988          0.13673871          0.05740561          0.04951662         -0.03940410          0.07655210          0.08887779          0.06360155         0.063447530          0.09165828          0.10386274         0.098671883          0.08994742          0.14845583          0.05137301         0.101763991        0.0439691905          0.12523626         -0.05949182         -0.02266147          0.04146871         -0.01734481          0.02456185        -0.005848951          0.11898178        -0.003748745          0.04014935         0.049498323        0.0378446673         0.028926994         0.081286268          0.06431596
astroglia_up                 0.13560615          0.06372746          0.09853784        -0.061051452          0.01577089         -0.04760733         -0.01301234         -0.02033879          0.03042881         0.007860558           0.1302317          0.04866147          0.11807311          0.02651416         -0.02576869         -0.02249800          0.03139450          0.01262743          0.10298674          0.04376961         -0.02441912          0.04007613          0.10426429          0.05984316          0.09531040          0.01361742        -0.006054302          0.01417130          0.01785855        -0.024485729          0.04885270          0.04978712          0.01089287        -0.003688539       -0.0255875216         -0.05318817          0.01572855         -0.04017804         -0.01581070          0.08027547          0.06475093        -0.019267885         -0.01000033        -0.012468882          0.03808888         0.016444129        0.0004891894         0.006058522         0.001277776          0.04623002
neuronal_up                 -0.01603674          0.03026768         -0.04846411        -0.081274578          0.03036729         -0.10588657         -0.04819897         -0.21472580         -0.07924660        -0.014852256          -0.3937604         -0.10090691         -0.42227945         -0.02226663         -0.03522747         -0.15937196          0.02880150         -0.03360695         -0.19537945         -0.02678998         -0.01237703         -0.05800257         -0.08946093          0.02804959         -0.33447989         -0.06646701         0.001490673         -0.06111592         -0.00788255        -0.005433944          0.08875419         -0.04552211          0.06832540        -0.054242676       -0.0165587308          0.03709143          0.08683758          0.07694510          0.00983925          0.05086959          0.03951686         0.046397028          0.03379387         0.065956603          0.07285765         0.002567756        0.0022974121         0.076873274         0.040563891         -0.04577361
oligodendrocytic_up         -0.09082646         -0.03209598         -0.06775336        -0.001343057          0.09570037         -0.04469363         -0.03506036         -0.09033811          0.01079102        -0.008493560          -0.1060987          0.02222565         -0.09131953         -0.02902642         -0.01525947         -0.07435504          0.08049313          0.05654690          0.03601434          0.01580467         -0.08981765         -0.01162585          0.03884722         -0.00640505         -0.11088869          0.06651459         0.048149691          0.05667692          0.06740432         0.057691526          0.05627159          0.01676310          0.06553035         0.068221314        0.0005776113         -0.02757186          0.07961760          0.03639202          0.08426877          0.07545897          0.07456736         0.040406936          0.06787397         0.080378144          0.05427988         0.059627054        0.0040825991         0.039001591         0.038807887          0.01393330
                    TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up                0.10254985        0.1209366458         0.005457102          0.05470414          0.05324132         0.004583494          0.07287897          0.01803334         0.092298928         0.106581126          0.03911847          0.08760433          0.08083304          0.12273304          0.08658859          0.09439140          0.12859993          0.12899656         -0.05799326         0.043791271         -0.12734557         -0.07620178        -0.101627927          0.07398850         -0.14128439          0.04168816         -0.10586947         -0.07738761         -0.05189054         -0.04129260        -0.029881354         -0.02425999         -0.03083819         -0.01363261         -0.03413866          0.03369514         -0.02533095        -0.026089207         -0.05887989        -0.023565388         -0.02660048         -0.13175535        -0.131223466         -0.04934655         -0.07222247          0.04595771        -0.002484733         -0.02006267         -0.02129216        0.0121870804
astroglia_up                 0.01473182       -0.0002823507        -0.041514372         -0.04221281          0.05781689         0.010362305         -0.03948686         -0.02292038         0.009218869         0.003819796          0.08805820          0.05787047         -0.04832227         -0.04771188         -0.03770525         -0.00397720          0.01702062         -0.04901255         -0.15053965        -0.066808334         -0.12029138         -0.13543562        -0.111383004         -0.11055588         -0.07080332         -0.05626645         -0.16040451         -0.06003255         -0.11320734         -0.07762499        -0.067457036         -0.06885981         -0.07206253         -0.09501078         -0.08210609         -0.14076913         -0.09259525         0.017705647         -0.07440865        -0.075879552         -0.10686648         -0.12383580        -0.109491916         -0.05092156         -0.12756381         -0.04676953         0.016467894         -0.08296504         -0.11449864       -0.0624475003
neuronal_up                 -0.05510838        0.0693924418         0.049907805          0.06579639         -0.03553495         0.060569667          0.04258533          0.05347991         0.011061722        -0.022561037          0.05657129          0.08324986         -0.06484210          0.05410708          0.08696189          0.04328396          0.04756120          0.05241028          0.03859840         0.004121992          0.05429824          0.06696186         0.039995573         -0.03731216          0.03871302          0.01346663         -0.02003846          0.03361013          0.08956373          0.05912840         0.004434217         -0.12181570          0.03493980          0.01353410          0.04421769          0.01083988          0.03740344        -0.008455138          0.03989240         0.043233261          0.03530835          0.04811405         0.067893057          0.06035066          0.05073357          0.04311893         0.074185702          0.05368352          0.04001603       -0.0368438811
oligodendrocytic_up          0.01488734        0.0588328752         0.073964840          0.05639762          0.06448371         0.103919757          0.05028910          0.07722783         0.094043741         0.035205083          0.07003096          0.06202171          0.04362975          0.05582357          0.08811635          0.07662414          0.06354034         -0.13317556          0.09801811         0.010237076          0.04782735          0.09917287         0.003572068          0.02818885          0.12062411          0.06959310          0.09380954          0.09824244          0.04046508          0.05673212        -0.016644605         -0.11809801          0.06714657          0.02817944          0.07503049         -0.01017455         -0.01208933        -0.031760653         -0.16273288         0.008979194          0.06577860          0.08468706         0.006857635         -0.03150528         -0.03036885          0.08254308         0.070749406          0.09400074         -0.01657986       -0.0003181655
                    TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up               -0.12793182          0.05813961         -0.02996638         -0.03999179         -0.01317216         -0.06556770         -0.06014645         -0.10524550          0.03410507          0.03174620         -0.07131517         -0.03864651         -0.00656357         0.004862977         -0.05760770         -0.03220225         -0.14379979         0.006209294          0.01015281         -0.02506194         -0.15712941         -0.06978470        -0.039842096
astroglia_up                -0.07509997         -0.03112873         -0.07460949         -0.10572792         -0.07367029         -0.08467325         -0.05192066         -0.04367356         -0.07272862         -0.06252615         -0.10738803         -0.07352765         -0.08211912        -0.086061829         -0.11834540         -0.05541622         -0.05335162        -0.071461495         -0.06913880         -0.14663735         -0.10229018         -0.04606975        -0.030543430
neuronal_up                  0.04965757          0.03625217          0.04174849          0.04119978          0.04325152          0.04343971          0.04604542          0.03545067          0.04582293          0.07345420          0.01598958         -0.00251816          0.03897229        -0.071738618          0.06571136         -0.05706466          0.03314141        -0.016854947          0.07308937          0.04576623          0.03139639          0.06476292         0.047577132
oligodendrocytic_up          0.06265322         -0.03057294          0.08799201          0.04420027          0.07389345          0.10096870          0.02276466          0.04904987          0.08861485          0.09026904          0.06005119          0.02120084         -0.02586168         0.056221418          0.04705479          0.02053537          0.11599128         0.059425833          0.04519846          0.09306496          0.10243557          0.07848995         0.009634767
> 
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+                                 grep("_DN$", names(c2BroadSets)))]
> leukPar <- plageParam(leukemia_eset, cgpC2BroadSets,
+                      minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
                                                  CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP                    -0.1733940255       -0.033909950        -0.21494771        0.225895163        0.063750234        0.167895761       -0.120141623       -0.301364574       -0.127897961        -0.17662816      -2.033307e-03      -0.0580768131         0.22143221        -0.10332109        -0.22150927        0.043353690        -0.25639842        -0.09207537        -0.08853224        0.026931498        -0.14639547        0.099528895      -0.0728970131         0.20132393        0.071949059        0.065447939         0.14428259        0.131615034        -0.13550381        0.058275958         0.32869002         0.11720023        0.110313219       1.576915e-01         0.36374728       -0.052301552       -0.221995813
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP                    0.0091056904       -0.007229294        -0.26682324        0.239296160        0.102079970        0.107282626       -0.220934366       -0.114993916       -0.242707246        -0.35282402      -1.319142e-01      -0.2908596517         0.19217905        -0.05096841        -0.30028124        0.081213713        -0.06235553        -0.03413274         0.14630064        0.233615255        -0.02563993        0.216233541       0.1512191200         0.18209821        0.096718310        0.012136911         0.05625600        0.144054943         0.15035428       -0.046779826        -0.05975187        -0.23316425       -0.056470909      -4.192709e-02         0.16251868        0.109530419        0.147564140
WINTER_HYPOXIA_UP                                       0.0834055313       -0.070653851         0.36411795       -0.247095973       -0.178229854       -0.221082475       -0.024371138        0.180921942        0.038462365         0.10271188      -6.399298e-02      -0.0082717873        -0.01821576         0.28000441         0.17834176       -0.050337001         0.11095592         0.07805238         0.10651755       -0.242836351         0.23470420        0.062017426       0.0444107834        -0.26140415        0.191019536        0.057727131        -0.25471951        0.003543483         0.20328048        0.027252717        -0.16090502        -0.15356573       -0.065566664       5.311727e-02        -0.35349585       -0.060628683        0.034808040
PYEON_HPV_POSITIVE_TUMORS_UP                           -0.1194662949        0.038017996        -0.28521866        0.275081686       -0.031488732       -0.038588970       -0.100533814       -0.297050611       -0.238634457        -0.29082863      -7.600985e-02      -0.2335338233         0.31515092        -0.08353618        -0.18336902        0.087151767        -0.20372452        -0.14291385         0.03273765        0.233092544        -0.04825298        0.113859039       0.0442618489         0.16991714        0.231386554        0.005267212         0.03397312        0.099018174        -0.04752945        0.167145951         0.12918791        -0.11535230        0.055991634       8.848689e-02         0.24812128        0.117475851        0.050707009
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP            0.1198739462        0.187824071         0.39422522       -0.345600421       -0.152731606       -0.106308076        0.142740956        0.120710037        0.111680385         0.07724317      -8.733673e-03       0.0899926339        -0.06187972         0.35041893         0.14911728       -0.027779682         0.08478613         0.05561965         0.01558144       -0.248802758         0.23046261        0.041120203      -0.0006047729        -0.26801992       -0.003634823        0.026561742        -0.21188895       -0.043144995         0.07637875       -0.133457745         0.15331729        -0.05186474       -0.076486263      -1.260192e-01        -0.25406257       -0.154880107       -0.151754404
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP                0.2252138709       -0.016371911         0.37845026       -0.211838619       -0.067003022       -0.082541632        0.107463748        0.354471664        0.050713686         0.05482788       3.898683e-02       0.0381826905        -0.26206483         0.04681314         0.14091476        0.033986348         0.26834682         0.12993489         0.11032619       -0.004324969         0.16729155       -0.004938875       0.0658737109        -0.21012140       -0.044233735       -0.047256310        -0.15738147       -0.115751643         0.13986387       -0.054860717        -0.29955088        -0.13555352       -0.170517674      -1.622639e-01        -0.29957850       -0.092711253        0.087202988
LU_TUMOR_VASCULATURE_UP                                -0.2378969459       -0.062771846        -0.34031239        0.168539328       -0.005657595        0.008190157       -0.167323313       -0.338981975       -0.012484156        -0.02906254       7.237425e-02      -0.0041181720         0.05644821        -0.09547833        -0.17278295       -0.026587364        -0.15721892        -0.08290324        -0.07692133        0.027096635        -0.15539443       -0.039807725      -0.0907044859         0.15741811        0.099085419       -0.025321125         0.12258506        0.194526161        -0.21552019        0.417930079         0.09449431         0.15446705        0.179506032       2.947411e-01         0.20435875        0.153196747       -0.067708347
KORKOLA_EMBRYONAL_CARCINOMA_UP                         -0.0648890101       -0.032521742        -0.09549351        0.129393718       -0.193203052        0.019756674        0.033055489        0.012090742        0.162133586         0.15343460       5.965502e-02      -0.0946327900        -0.14723402         0.14926621         0.08055377       -0.069317678         0.09878785         0.05716404         0.27551849        0.032230796        -0.22770260       -0.151166173      -0.2096628767        -0.10471736        0.361843632       -0.171443414        -0.17937880       -0.066953233         0.01485418        0.028228846        -0.09265788        -0.07985186       -0.145152990       5.837802e-01        -0.10747460       -0.064683118        0.046388878
KORKOLA_TERATOMA_UP                                     0.0246879829        0.314207438         0.37605979       -0.179124841       -0.032379168        0.129238282        0.172225286        0.235548971       -0.014739292         0.16769097       1.663879e-01       0.0188106200        -0.04650602         0.01986651         0.08451226       -0.166920945         0.17295139         0.03802788         0.12813343        0.126220125        -0.18602937       -0.161481817      -0.1742658425        -0.24643129       -0.122836999       -0.327714071        -0.29192403       -0.145207142        -0.09418954        0.059783879         0.09598647        -0.03320679        0.003223224      -1.181121e-01        -0.17877126        0.090599349        0.095678786
KORKOLA_YOLK_SAC_TUMOR_UP                              -0.0007555054       -0.021421796         0.02632694       -0.035433567        0.141613226        0.019911372       -0.004796058       -0.001649931       -0.102005325        -0.05763990       3.689459e-05       0.1935898594         0.20317659        -0.19638421        -0.08784612        0.042714637        -0.07671928         0.02373285        -0.34386769        0.028515433         0.18531115        0.075685824       0.1123704848         0.11078104       -0.341628831        0.120190881         0.08150623        0.099416803        -0.10395047       -0.040783114         0.10255693         0.11340823        0.112870194      -6.356078e-01         0.19628606        0.082304700       -0.021816705
KORKOLA_CHORIOCARCINOMA_UP                              0.1041128574        0.050802605         0.08356868        0.002616351        0.166705865        0.029083321        0.033339356        0.034863888       -0.145879153        -0.07857234      -1.949332e-02       0.1514434265         0.20246406        -0.23759405        -0.08452061        0.043151694        -0.08551227        -0.03830657        -0.31848162        0.011160018         0.16614410        0.086788071       0.0890085722         0.08732890       -0.362402733        0.121010372         0.11882511        0.112394298        -0.10527127       -0.045309504         0.09942631         0.07787554        0.114541375      -6.194077e-01         0.15411825        0.063366395       -0.063388257
KORKOLA_SEMINOMA_UP                                     0.0143883280       -0.061538315        -0.07332409       -0.002029272        0.217358315        0.098241098        0.032751796       -0.087814242       -0.081314491        -0.06460506      -5.616862e-03       0.1630969932         0.21820386        -0.21452236        -0.11089417       -0.032477859        -0.09300386         0.04122480        -0.28319229        0.073437921         0.09605443        0.020087468       0.1290883909         0.12890302       -0.381385908        0.084072436         0.16921641        0.055552661        -0.12958319       -0.053707297         0.10910509         0.13519677        0.161922009      -5.578087e-01         0.23735022        0.103641126       -0.056075120
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP       0.1123404419       -0.099246059         0.29251507       -0.325596653       -0.052662019       -0.012940114        0.154217301        0.308497258        0.189224705         0.17168566       1.231780e-01       0.1182710250        -0.19858688         0.12426680         0.23060251       -0.113059070         0.23861910         0.12627316         0.13843072       -0.039936738         0.03939179       -0.122691635      -0.0569411621        -0.14852082       -0.101765053       -0.037504955        -0.13765046       -0.140529751         0.04455761       -0.014788011        -0.25402909        -0.05853212       -0.116016632      -4.783914e-03        -0.41905900       -0.014673495        0.057442498
HOLLMAN_APOPTOSIS_VIA_CD40_UP                          -0.1151565209        0.052711436        -0.29807776        0.247422702        0.147590241        0.055423242       -0.142427543       -0.297218464       -0.186224424        -0.20741716      -1.121865e-01      -0.0760119941         0.24124543        -0.14203473        -0.20234670        0.043247386        -0.27180186        -0.07873619        -0.18050744        0.114991470        -0.02127029        0.167118090       0.0958585482         0.22051043        0.002936958        0.072780412         0.15534893        0.139476566        -0.15101819       -0.017452203         0.18358194         0.10429137        0.142368910      -3.065258e-02         0.33247353        0.112098951       -0.100935977
LIU_PROSTATE_CANCER_UP                                  0.2174486111       -0.073496729         0.28573856       -0.124499192       -0.057239993       -0.020429757        0.140693421        0.407214699        0.120220601         0.12989182       2.508589e-02       0.0967480905        -0.25967413         0.13919891         0.19209378       -0.031730039         0.24893454         0.09710975         0.17247772       -0.030756115        -0.11270677       -0.121554641      -0.0857006060        -0.09446246        0.010098924       -0.184232968        -0.21029038       -0.115727215         0.11745326       -0.045479539        -0.29983687        -0.12332926       -0.224404303      -3.488958e-05        -0.24405810       -0.081462154        0.140697510
LIU_SOX4_TARGETS_UP                                     0.0348520543       -0.161469634         0.26274156       -0.304202295       -0.050685124       -0.053041216        0.085962358        0.301189290        0.166324484         0.13116039       1.100475e-01       0.0647346500        -0.33897362         0.04852868         0.24684466       -0.016577714         0.23365434         0.07455878         0.16613184       -0.016965465         0.02436819       -0.227625669      -0.0004191321        -0.12194013       -0.111578239       -0.041314905        -0.09052165       -0.097587342         0.17721669        0.085952083        -0.28194043        -0.05932238       -0.057205746       5.321372e-02        -0.36367249       -0.015363998        0.142925944
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP          -0.0934159787        0.060976175        -0.26757898        0.202795542        0.127852418        0.116405632       -0.105679519       -0.207537683       -0.127761790        -0.21806297      -8.009341e-02      -0.0570496808         0.35572293        -0.16622240        -0.23033722       -0.003656037        -0.24351471        -0.08281439        -0.21385192        0.089045910         0.05702248        0.162830271       0.1073197522         0.18581478       -0.043297663        0.140169126         0.16915870        0.130244227        -0.19356051       -0.078973917         0.21181563         0.09276215        0.124145090      -2.047438e-01         0.27452947        0.097684909       -0.088142625
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP               -0.2531769445       -0.076391547        -0.35524046        0.178419647       -0.027932256       -0.062111318       -0.190294011       -0.401869438       -0.047034396        -0.09050315      -7.353341e-02      -0.0001531211         0.17442433        -0.05326287        -0.19853240       -0.023615069        -0.28054125        -0.06056164        -0.13689646       -0.006535930        -0.05171414        0.065779649       0.0174894144         0.18666747        0.145560303        0.080587372         0.12046867        0.174873906        -0.04655476        0.182351256         0.20782555         0.13377643        0.169157456       1.914065e-01         0.28928058        0.137016903       -0.018630858
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP               -0.1411454025        0.047900582        -0.25625196        0.269176774        0.181462253        0.034784740       -0.116174263       -0.301870796       -0.044968652        -0.14811820      -8.208908e-02      -0.0352154619         0.29059194        -0.07287436        -0.20680686        0.017363938        -0.30032548        -0.11323896        -0.17005992        0.006601310        -0.06746557        0.077409057       0.0159590455         0.26558390       -0.037694782        0.167440913         0.21207543        0.140875368        -0.19160167       -0.060321378         0.24086742         0.10370036        0.094599476       2.850367e-02         0.28597165        0.029669499       -0.164314548
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP                    0.1116529885        0.292188184         0.34831334       -0.123581722        0.050516147        0.145019714        0.206187041        0.163406743        0.007821523        -0.09940156       4.141215e-02      -0.0228886983        -0.05491470        -0.03095383         0.10860314        0.072183090         0.13099797         0.06711451        -0.07673696        0.041966891         0.25476428        0.177618166      -0.0154400900        -0.13870532       -0.100030138       -0.108760557        -0.10667785       -0.165118186        -0.21136962       -0.308830865         0.01307193        -0.01994302       -0.006007855      -5.126714e-01         0.03798671       -0.170143211        0.001351049
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP                     0.2745402112       -0.044177556         0.31876654       -0.329339068       -0.105691495       -0.142140913       -0.003162191        0.157173800        0.089932849         0.07302904      -1.286126e-02       0.0758662612        -0.43830863         0.10777430         0.12826241        0.012040783         0.27425517         0.11749725         0.05930217        0.038952950         0.07519665       -0.100333208       0.0973981350        -0.10538721       -0.085077261       -0.021507687        -0.12994877       -0.094083007         0.20864101       -0.006430176        -0.19660903        -0.01719751        0.009752194      -1.663727e-01        -0.31852933       -0.004341272        0.203116535
FRASOR_TAMOXIFEN_RESPONSE_UP                            0.2257957178        0.048434395         0.37131451       -0.247543764       -0.045657194        0.045635878        0.177470440        0.343445989        0.118508293         0.14408488       1.239577e-01       0.0438059242        -0.29647471         0.08855053         0.19195553       -0.026278996         0.24448407         0.11560848         0.07867322       -0.017378686         0.01098018       -0.168135671      -0.0825024498        -0.12893972       -0.172576527       -0.076678534        -0.18549006       -0.155205808         0.02425944       -0.011353726        -0.15818606        -0.07181830       -0.088612281      -2.797678e-02        -0.36273060       -0.104253429        0.030828162
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP                  -0.2233367530       -0.007741796        -0.37463807        0.260361044        0.062097031        0.042551473       -0.111730786       -0.361252426       -0.028706282        -0.04328331      -4.884767e-02       0.0149329143         0.25979025        -0.12316554        -0.20828246       -0.016039857        -0.15973390        -0.13573929        -0.06858283        0.107131118        -0.19184527        0.008118677      -0.0431836820         0.18748450        0.078381562        0.029201247         0.23179224        0.070307687        -0.20823179        0.030900475         0.23092058         0.16884357        0.117332432       1.166270e-01         0.32408086        0.047668182       -0.034181119
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP                    0.1108356219        0.072625095         0.35562137       -0.266060947       -0.107490386       -0.048812016        0.183603465        0.203732983        0.195010034         0.30190337       5.026785e-02       0.1833451993        -0.21665967         0.10730554         0.19889431       -0.080954542         0.22126893         0.13154304         0.03614184       -0.220001339         0.11292678       -0.131457134      -0.0455743876        -0.27755754       -0.067880624       -0.016925423        -0.14254500       -0.174080097         0.03526815       -0.091897678        -0.03194165         0.07521659       -0.066452401      -4.426222e-02        -0.30126507       -0.155867534       -0.087824518
WATANABE_COLON_CANCER_MSI_VS_MSS_UP                     0.1604393078       -0.046725031         0.24421714       -0.212744255       -0.088335734       -0.062050470        0.127640749        0.301282112        0.079637731         0.15503451       6.223935e-02       0.0203861980        -0.31159126         0.10664368         0.22892309        0.049192090         0.18292270         0.10162373         0.19409459       -0.004813772        -0.08510377       -0.099590371      -0.1592289695        -0.14987100        0.008425516       -0.293152578        -0.28643062       -0.040028563         0.18403042        0.088763148        -0.17183112        -0.07892018       -0.072561676      -5.959037e-03        -0.33781668        0.018589804        0.192669206
> 
> proc.time()
   user  system elapsed 
 56.562   1.354  57.905 

GSVA.Rcheck/tests/test_plage_newapi.Rout.save


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> 
> ## 2023-11-10  axel: simple test script for method PLAGE, new API
> 
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    expand.grid, I, unname

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db


> library(GSVA)
> 
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
> 
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
> 
> p <- 10000 ## number of genes
> n <- 30    ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+             dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
           s1         s2          s3         s4          s5
g1  1.4171739 -1.3444519 -0.99052898  0.4203395  1.30716224
g2 -0.7281951  0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754  0.09779699 -0.6792548 -0.09124045
g4  1.0735382  1.3156255  0.15588330 -1.8079608  0.48531108
g5  0.7229884 -0.9162342  1.93982245  0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+                    paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> plagePar <- plageParam(X, gs)
> plage.es <- gsva(plagePar, verbose=FALSE)
> dim(plage.es)
[1] 100  30
> plage.es[seq.int(min(nRowsToPrint, nrow(plage.es))),]
               s1           s2            s3            s4          s5           s6           s7           s8          s9          s10         s11           s12         s13         s14         s15          s16         s17           s18           s19          s20         s21          s22          s23          s24          s25          s26         s27         s28          s29         s30
gs1  -0.029219588  0.134185958  0.3713074711  0.0407816079  0.06092767 -0.220481051 -0.263761945  0.150320487 -0.22409656  0.009584613 -0.39111762 -0.1302648585 -0.05959038  0.33696215 -0.07282788  0.073310843  0.05147115 -0.2483084427 -0.0858324287  0.178309261  0.38540679  0.046642663  0.122541902  0.015905580 -0.097924551  0.029203351 -0.06630956 -0.07126728 -0.194205126  0.14834577
gs2   0.009713309 -0.070894760  0.0887748898  0.0438945086  0.07597568 -0.099232840  0.257432656 -0.180783042 -0.26082831 -0.191077787  0.03035706 -0.1035337259 -0.19412605 -0.10714563  0.07146483  0.086637398  0.20308822  0.0140285507 -0.2137568863  0.239387383 -0.22371195 -0.206819710 -0.133382606  0.108114986 -0.046079067  0.089875594  0.42299690  0.41937892  0.096947556 -0.22669608
gs3  -0.139922266 -0.117741577 -0.0781834024 -0.2165908186  0.27378251  0.311048702  0.086846172  0.044475856 -0.08203218  0.119527132  0.03846745 -0.2109524281  0.12655940 -0.38507377  0.10369939 -0.017494211  0.16994906 -0.1420728947 -0.0785235706  0.004983979 -0.08761015  0.009889028 -0.094132008 -0.247835746  0.083711263 -0.250047995 -0.11800166  0.26164152  0.264615361  0.36701785
gs4   0.136784356 -0.055804012 -0.0003340026 -0.1516269802 -0.27114196 -0.083083560 -0.096565517  0.036868895 -0.06300502 -0.221561203 -0.19813522  0.1042473505  0.08093850  0.05674063 -0.19895817  0.067302708  0.25451893 -0.0005207089 -0.1159880895  0.048467793 -0.20603836  0.159545022  0.044036214  0.534771648  0.105886354 -0.017032347  0.07891909 -0.39111885  0.312125306  0.04976120
gs5   0.034934164  0.039749845  0.1228855856 -0.2732261283  0.04199286  0.103214014 -0.195436449 -0.287379571  0.03966687  0.303622722  0.07474143  0.0856083346  0.13595773 -0.01383837  0.35831980 -0.051209828 -0.43727399  0.1718981370 -0.1181945240  0.089941405  0.27917773  0.023292236  0.118740362 -0.297527028 -0.070561479 -0.048431187  0.02429263 -0.23305662  0.114527349 -0.13642802
gs6  -0.279844320  0.191897986 -0.3053996126  0.0094415284  0.04842640  0.194020478  0.096966418 -0.068898812 -0.20073135  0.378243740 -0.19309702 -0.1466213408 -0.14129713 -0.26167877  0.16969940  0.003873402 -0.06359659  0.1923023239 -0.2857295678 -0.037571361 -0.13741602  0.028278539  0.238658744 -0.074846882  0.198735207  0.142033651  0.30737897 -0.09691484  0.003752428  0.08993441
gs7   0.225539026  0.254315627  0.0211474628  0.3655580391  0.12888554  0.040475802 -0.108671963 -0.177723642  0.41116878  0.227671549 -0.28572797 -0.0471024585 -0.11298848 -0.14563561 -0.04101156  0.001529252 -0.30955146  0.2015628322 -0.0515248852 -0.202779772  0.26345240 -0.037525716 -0.006683093  0.089664221 -0.112755956 -0.152690537 -0.11819571 -0.06373540 -0.095213785 -0.16145252
gs8  -0.231283677 -0.053675557  0.0264131810  0.1359540470  0.08233788 -0.227928562 -0.087182432 -0.090687865 -0.08943693  0.307308887 -0.26623882  0.0138228392  0.21217554 -0.01320852 -0.37951349 -0.052096781  0.10783552  0.1598299126 -0.2189896514 -0.112309675  0.24977969 -0.065970466  0.140396761  0.076196677 -0.330320943  0.135782120  0.26952133  0.29550850 -0.055760954  0.06174143
gs9  -0.149696707  0.070112664 -0.3927757978  0.0404540759  0.05022070  0.286507502 -0.292734447 -0.111830390  0.01797344 -0.123194982 -0.12329977 -0.0405767884  0.05003308  0.38368419  0.01421485  0.062677869 -0.07909931  0.0486677864  0.0095880253  0.132223596 -0.28737944  0.178169340 -0.379773116  0.242912453  0.188194766  0.217203390  0.11001738 -0.02903181 -0.001529958 -0.09193259
gs10 -0.117672007  0.025542827  0.1308302520 -0.1626636222 -0.09699436  0.244461645  0.359249078 -0.191834856  0.03983472  0.146795086  0.06267437 -0.0434347372 -0.04176742 -0.06732570  0.13904093 -0.305077580 -0.02187673  0.1570480436  0.1334628532 -0.279021420  0.06938138  0.363531649 -0.201888466  0.258009015  0.084167939 -0.202884988  0.12079417 -0.11859744 -0.252643549 -0.23114107
gs11 -0.117405216 -0.048550062 -0.2152359244  0.1765495035 -0.15055137 -0.123720213  0.102298045 -0.027754231  0.20009873  0.250537460 -0.05653296  0.5188172981 -0.14533038  0.18956907 -0.05111332 -0.028603358 -0.08113559 -0.1326973408 -0.2163548884  0.153306782 -0.24927555  0.377259651 -0.143092985 -0.138807673 -0.201352437 -0.049677679 -0.09122352  0.11203847  0.069118818  0.11882086
gs12 -0.543671749 -0.184614928  0.1099977497 -0.0553393639 -0.40340420  0.033822756  0.082140727  0.090566044  0.06267315 -0.035981570  0.18191246 -0.1165185323 -0.14432586  0.18146646  0.03547440  0.236193030  0.02238259  0.0383756956 -0.0935119488  0.043760861  0.02041612  0.063399434  0.120073412  0.080158878 -0.122419354  0.011193111  0.21268970 -0.20265505 -0.123185463  0.39893143
gs13 -0.024887916  0.118584422  0.1388041889 -0.1413124768 -0.39825505  0.052045207  0.261267389 -0.255779352  0.08983137  0.244926313  0.25970077 -0.0188348892 -0.36760612 -0.01271960 -0.20002981 -0.087057056 -0.05944590 -0.1591285151  0.2077404356  0.302011283 -0.02371886  0.178685780  0.016103242 -0.065410956  0.141870716 -0.181431006  0.21774895 -0.11979818  0.016494216 -0.13039859
gs14 -0.100340055  0.077189402  0.0390858762 -0.0370017538 -0.38389060  0.184412799 -0.118805404  0.151984291 -0.25219352 -0.107177720 -0.13513101  0.0625168832 -0.10590181 -0.17815359  0.03224044  0.159411109 -0.08896745 -0.1280661493  0.1577303651 -0.038406698 -0.27702921 -0.122279723  0.239019808  0.128024840  0.212749941  0.142712690  0.18985273 -0.29773955  0.378010038  0.21614304
gs15  0.048774560  0.060119682  0.0484913743  0.2519843778  0.03039694 -0.234375681 -0.108291508 -0.453456336  0.06303550  0.086507823 -0.04349266  0.0260079589 -0.07031311 -0.07260948  0.19503960  0.264057607  0.30593891  0.1027550963  0.2715334959 -0.065807601 -0.15451764  0.253065015 -0.142033610  0.149114814 -0.156868088 -0.142545833 -0.28141243 -0.15529889  0.134277793 -0.21007769
gs16 -0.121838108  0.078038618  0.1774058118  0.3701311334 -0.27325953  0.179212470 -0.183228978 -0.297884469  0.07431105  0.142904264 -0.37912167  0.0392912596  0.31140398 -0.15567324  0.30015891 -0.075661103 -0.09261959  0.0039456916 -0.0540112724 -0.046884108  0.18371220 -0.073575237  0.236113549  0.114082325 -0.059486224 -0.043877650  0.05583114 -0.19847973 -0.131850692 -0.07909080
gs17  0.184799857  0.070052354  0.3514429664  0.1732326612 -0.22022967  0.003214861 -0.405239687 -0.047291743 -0.24679440  0.160056459  0.08518827 -0.0463285866 -0.06034854 -0.30001767 -0.19348991 -0.035213712 -0.09465668  0.0759894988  0.1785756235 -0.132155045 -0.17500659  0.376832927  0.013218793  0.018574170 -0.110793912  0.229997712  0.16584921  0.05705518 -0.156772307  0.08025791
gs18 -0.187087483  0.337139118  0.1688542303  0.1173035568  0.05984658 -0.185941480 -0.119363637 -0.382728482 -0.15395065 -0.319451357 -0.19733920 -0.0144161899  0.24873343 -0.10552473  0.04524322 -0.001873581  0.22373606  0.0229936448 -0.3542996024  0.061859205  0.02839072  0.078164766  0.344304336  0.045874812  0.009125945  0.025623338  0.17909395  0.09353534 -0.131011234  0.06316538
gs19 -0.059003209 -0.199168662 -0.1837419847 -0.2237610050  0.39738058 -0.326919064  0.087628623  0.181877873  0.35191549 -0.027680315  0.24795143 -0.1101431952 -0.01839169 -0.16235495  0.08701808 -0.090546490  0.16014091  0.1263778250 -0.0780805378  0.230737817 -0.22144812 -0.217901043 -0.019311240 -0.228211869  0.086283799 -0.067073673  0.17863523 -0.10809469  0.095046484  0.11083758
gs20 -0.087459182 -0.195412041 -0.0130357705  0.2848639974  0.22802341 -0.158851672 -0.203819293 -0.074651734  0.26441584 -0.163246538 -0.16645128 -0.0007860099  0.23034725 -0.10381161 -0.44439333  0.400370645  0.17176277  0.0072304296 -0.0820074325  0.083326015 -0.18145094 -0.041971647  0.076837721  0.000302442  0.174386727 -0.151895543 -0.01190509  0.10267278 -0.134531574  0.19114066
gs21  0.107602195 -0.142208461 -0.1560412602  0.1057618700  0.08242831 -0.094411152 -0.402862002 -0.372859070  0.03195170 -0.056225322  0.02369290 -0.0133280573 -0.19355100 -0.27795918 -0.03191200  0.364990768  0.28739587  0.1564537944  0.0719681085  0.169215470  0.29072561 -0.251367594  0.063227672  0.159273607 -0.096533492  0.163138228  0.01013211 -0.06972215  0.049191913  0.02183063
gs22  0.281156732 -0.185969190  0.1466983344  0.0988277638 -0.05639434  0.008345487  0.314359229 -0.035846835 -0.02674254  0.048462980  0.04194433 -0.2929134701 -0.02180503  0.16130641 -0.09628426  0.094556572 -0.17393215 -0.0501843811  0.0418822082 -0.042590804  0.17563655 -0.241418448  0.454068984 -0.195659705 -0.078786970 -0.020000914 -0.31312338  0.24019694  0.013901423 -0.28969152
gs23  0.287000160 -0.009577127 -0.0258026809  0.3978394227  0.06574872  0.165351593  0.202895394 -0.008028034 -0.07998444  0.210698794  0.07377611 -0.0586860376 -0.15454336  0.13418397  0.08296051 -0.055745695 -0.06072953  0.0004303990 -0.0731050722 -0.109362156  0.03413574 -0.043312239 -0.067080708 -0.310656179 -0.124265593 -0.262454623 -0.54504850  0.22851199  0.123089583 -0.01824042
gs24  0.226216800 -0.073685267 -0.0417664264 -0.0006964549  0.18170065  0.466969874  0.008804967 -0.038827882  0.15703216 -0.158480858 -0.21933991 -0.0418454781  0.08244118  0.05264244  0.19388981  0.261405034 -0.08604337 -0.2537728142  0.0002742249  0.022868190 -0.15317303 -0.197659709  0.102648478  0.127786731 -0.008318546 -0.272121666  0.17408086  0.09227398 -0.213205479 -0.39209848
gs25 -0.227611755  0.023775737  0.0723240408 -0.1495365735  0.06081540 -0.172945821 -0.104641914 -0.283228744  0.09443370  0.264032568 -0.30609675  0.1905985693 -0.15253022  0.33940139  0.05489225  0.083252511  0.19734533 -0.0236399481  0.2777489932  0.036835483  0.17108518 -0.190520756  0.150268031 -0.160683713  0.167731621 -0.006525896  0.10202510  0.02616628 -0.376857271 -0.15791283
> 
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+                     featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+                     sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+                                       grep("^REACTOME", names(c2BroadSets)),
+                                       grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- plageParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+                       minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
                                                    NA19099     NA18523     NA19144     NA19137     NA18861     NA19116      NA19130     NA19131     NA19119     NA19152      NA19153      NA19140      NA19138      NA18522      NA19192      NA19193      NA19239      NA19238      NA19210     NA19201     NA19172      NA18870     NA18858     NA18852     NA19159     NA18855     NA19204     NA18501     NA19127      NA19098       NA19093      NA18856      NA18912       NA18517     NA18502       NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                  0.11442430  0.32079541  0.19023827 -0.16386259 -0.34124516 -0.08626990  0.006244354 -0.09133096 -0.07958067 -0.19080877 -0.129759539 -0.011392352 -0.053528324  0.137113192  0.122790549  0.185113826  0.255475291  0.289729331 -0.231805083 -0.10599439 -0.16563165  0.254730153  0.28736502 -0.07380857 -0.13262739 -0.00202695 -0.12848634  0.04738066  0.15451669 -0.042949836 -0.1917455098 -0.158789670 -0.030545427  0.1681240794 -0.02372029 -0.0981317670
KEGG_CITRATE_CYCLE_TCA_CYCLE                    -0.14376128 -0.40210177 -0.10732752  0.22556600  0.22044109 -0.04149364  0.082632466 -0.03088703 -0.10141600  0.21634351 -0.099937129 -0.238283100  0.059799913 -0.044056815  0.106146035  0.035855219  0.056963046 -0.091694988 -0.111915190  0.08270476  0.17136294  0.002778763 -0.17116078  0.04310892  0.38606731  0.26041385  0.18985748 -0.28660545 -0.22184771 -0.072806417  0.0353622058  0.097891536 -0.169106885  0.1413099205 -0.11591220  0.0357089449
KEGG_PENTOSE_PHOSPHATE_PATHWAY                  -0.16235500 -0.32582108 -0.11076423  0.23827639  0.33496725  0.02867445  0.017174780  0.06591909  0.10482653  0.18448109  0.051993550 -0.025185654  0.117266799 -0.086462365 -0.121860074 -0.309601472 -0.202595001 -0.203907440  0.166706699  0.13841854  0.05621760 -0.217255930 -0.23400863  0.03480311  0.03693621  0.18017005  0.17067361 -0.14698325 -0.15401687 -0.039631290  0.1852566211  0.251925461  0.059502652 -0.1710616230 -0.05714658  0.1444660100
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS   -0.19045563 -0.30144436 -0.06208281  0.23907573  0.23514442 -0.11949500  0.256530147 -0.15784897 -0.07002696  0.18754970 -0.156566301 -0.233437891 -0.028875826 -0.135832499  0.007013319 -0.063573306 -0.045190431 -0.134951243 -0.119095747  0.08957830  0.20494217  0.014625096 -0.21685204  0.12579094  0.30068903  0.30284667  0.20017848 -0.22704585 -0.03911287  0.152821859 -0.0118501734  0.195309455 -0.129960080  0.0414442346 -0.05624288 -0.0535986719
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM             0.08708061  0.36924639  0.16317478 -0.18733952 -0.22969884 -0.07403687  0.005513622 -0.13403336 -0.10757766 -0.11347043 -0.126968905 -0.068529526 -0.073097377  0.145409314  0.117559506  0.192280283  0.262745324  0.261030448 -0.187064190 -0.10806619 -0.21446933  0.264815017  0.32316348 -0.02316450 -0.08242710  0.09121413 -0.08115837 -0.06082489  0.05128248 -0.096144492 -0.1729482337 -0.179767986  0.079378632  0.2025544282 -0.14107384 -0.1545868541
KEGG_GALACTOSE_METABOLISM                        0.13896759  0.33236986  0.15287628 -0.19570500 -0.37392490  0.03112239 -0.101122302 -0.02357435  0.03161318 -0.18551649  0.042859194  0.003683625  0.058836073  0.058593014  0.103013057  0.136717007  0.125649307  0.257519495 -0.059380958 -0.09369887 -0.16262023  0.145102780  0.38948984 -0.18103028 -0.24299641 -0.04474028 -0.20609816  0.05089387  0.23425714 -0.067198742 -0.1327201321 -0.208840024 -0.007338931  0.1015346567  0.02976531 -0.1383576213
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM           0.08699846  0.02769904  0.03088309 -0.15783874 -0.16132270  0.07393045 -0.152562581  0.17928005  0.15457917 -0.11563182  0.248868576  0.203636007  0.038899707  0.177895808 -0.087598070  0.024330837 -0.068874923  0.166621148  0.195566178 -0.09919733 -0.51840256 -0.125338656  0.15816739 -0.06627634 -0.24722350 -0.12644374 -0.27029081  0.23656458  0.03682528 -0.172195675  0.1255991760  0.010036282  0.146200884 -0.1183297380  0.06921028  0.0957347869
KEGG_FATTY_ACID_METABOLISM                       0.25246920  0.21487789  0.06756412 -0.24015561 -0.15971798  0.04164973 -0.134634522  0.18133621  0.18742246 -0.09879733  0.059789040  0.211657105 -0.189741758  0.051073442 -0.063493728 -0.055876110 -0.064518498  0.032865183  0.144745872 -0.12747677 -0.34740988  0.017286592  0.07659859 -0.12250954 -0.14145045 -0.32332540 -0.30311340  0.30156896  0.14235300 -0.020396100  0.1491018982 -0.054180990  0.209632783 -0.0622606872  0.15856855  0.0084981268
KEGG_STEROID_BIOSYNTHESIS                       -0.26848204 -0.15151075  0.27196342  0.20005723  0.05633948  0.06709033 -0.076856972 -0.08144521 -0.11182014  0.23060319  0.031572540 -0.043182612  0.162334518 -0.113794316 -0.221396081  0.039299968  0.198596097 -0.125931968 -0.101950870  0.12788728  0.03906626  0.135077658 -0.01696710  0.13279903 -0.12493729  0.40294067  0.30898303 -0.07471426 -0.07229951 -0.346954681 -0.0425758777 -0.008173547 -0.157861540 -0.0398692105 -0.24333940  0.0194526802
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS              0.22788265  0.27727244  0.12605512 -0.15231262 -0.07420505  0.10099690 -0.110400990  0.02784962  0.28647176 -0.07980438  0.173249992  0.174422862 -0.001563672 -0.107332599 -0.175605638 -0.211736911 -0.291012627  0.054097637  0.082675881 -0.19222910 -0.13208641  0.074845949  0.13658238 -0.04373454 -0.29216427 -0.25438809 -0.14526442  0.35661858  0.13638691  0.113474381 -0.0882569668 -0.027551600  0.137701542 -0.1643334547  0.08505740 -0.0276586587
KEGG_STEROID_HORMONE_BIOSYNTHESIS                0.22975311 -0.04610095  0.10063919  0.12299358  0.03877036  0.13465162  0.088715672  0.03494038  0.14951930 -0.05843410 -0.117297356  0.306369502  0.111144794 -0.204491028 -0.060894682 -0.033714074 -0.112850883  0.124922513 -0.016199947 -0.31755512 -0.07037955 -0.124619972  0.26355333 -0.17914396 -0.22832643 -0.07349334 -0.47727891  0.09134310  0.19265056  0.233158643 -0.0247334479  0.032853743  0.146944492 -0.1899024173 -0.01884571 -0.0486620136
KEGG_OXIDATIVE_PHOSPHORYLATION                   0.04757384  0.42969714  0.09223380 -0.31361918 -0.22482181  0.17872708 -0.156175716  0.03456549  0.07932693 -0.18222063  0.263950703  0.156720262 -0.054368092  0.125986316  0.006787002 -0.084583991 -0.046388261  0.156195922  0.171548956 -0.20861678 -0.19200932 -0.036138327  0.17882865 -0.06323935 -0.25938295 -0.15467774 -0.19415965  0.14534418  0.07217123 -0.002104513 -0.0639220237 -0.134737904  0.153885773 -0.0408505217  0.22491981 -0.1064463186
KEGG_PURINE_METABOLISM                           0.20065318  0.29721544  0.19035916 -0.18768395 -0.14876802  0.07499662 -0.111130384  0.04279520  0.10058079 -0.18253753  0.104394237  0.237489023 -0.156272735  0.004695238 -0.018444109  0.010848786 -0.031681573  0.100509407  0.200116332 -0.20128343 -0.13295068  0.008116163  0.13517872 -0.16149991 -0.22650307 -0.34997849 -0.25612139  0.34931922  0.23373805  0.081067825  0.0055786780 -0.137452124  0.043582088 -0.1302252071  0.06943792 -0.0581394776
KEGG_PYRIMIDINE_METABOLISM                       0.21386387  0.31876668  0.13823771 -0.14977881 -0.22350466  0.05640788 -0.109066678  0.08462733  0.05200829 -0.09300310  0.030350113  0.314550177 -0.257314444  0.018989332  0.005829506  0.037731104  0.070314765  0.162687671  0.059216742 -0.19130213 -0.19705259  0.038453179  0.10999248 -0.11951467 -0.20321833 -0.33534029 -0.21755611  0.34102133  0.23875776  0.060935006 -0.0074629043 -0.180715242  0.033546687 -0.0939514779  0.01458195 -0.0220880991
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM -0.20681031 -0.37748716 -0.12565805  0.26798513  0.26914186 -0.12685519  0.153416637 -0.01650182 -0.14404837  0.28618661 -0.253033160 -0.185735835  0.033980001 -0.059404347 -0.042798179  0.052827743  0.087918043 -0.047097005  0.002603537  0.12045456  0.02098204 -0.038730195 -0.18413718  0.08243411  0.13850374  0.35054894  0.23717572 -0.12482694 -0.12337093 -0.048174199  0.0483989160  0.232747019 -0.087796534  0.0098209646 -0.20356325  0.0009030612
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM     0.01555983  0.39948710  0.26524975 -0.11344673 -0.30536311  0.13871948 -0.119877999  0.01826166  0.03199101 -0.13884023  0.000402732  0.228057870 -0.065492316  0.046027102 -0.120910813 -0.112044381  0.107682776  0.280525919  0.062717644 -0.08761679 -0.31120689  0.045531608  0.16292802 -0.12689384 -0.31176258 -0.11566649 -0.04943121  0.14634414  0.17297063 -0.064286408 -0.1019910400 -0.192809929  0.239116210  0.0222125604 -0.07591641  0.0297711570
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM          0.14011533  0.44950137  0.13715860 -0.21286365 -0.25951992  0.03554671 -0.035671613 -0.01235037  0.10835898 -0.19692749  0.119707919  0.229911107 -0.124986706  0.071248763 -0.050382477  0.112207174 -0.038781286  0.141432934  0.158050492 -0.24246930 -0.20193494  0.019331667  0.10357964 -0.11758175 -0.13149796 -0.30066366 -0.23406437  0.28585381  0.13769399  0.074084706  0.0009278377 -0.149035605  0.067135796 -0.0470514419  0.08543382 -0.1214980980
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION   0.18341492  0.34228948  0.05029107 -0.34818659 -0.10685182  0.09265336 -0.088466493  0.11016160  0.15517234 -0.26698602  0.224420582  0.146464701 -0.044408678  0.093719606  0.048431770 -0.038893096 -0.147876699 -0.001782784  0.121902396 -0.03997209 -0.15444379 -0.033776069 -0.00457758 -0.03957663 -0.17241854 -0.33220603 -0.31794663  0.27603631  0.13609807  0.092390238  0.0150196645 -0.116601679  0.108012207 -0.1542070774  0.21229246  0.0004075145
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS -0.14556385 -0.10361716  0.22024326  0.31503617  0.06126010 -0.11154855  0.086414704  0.09990315 -0.15911865  0.25419971 -0.371443880  0.088126533 -0.008249792 -0.058022569 -0.290894975 -0.038124927  0.289981591  0.243192257 -0.230345230 -0.15276445 -0.12892010  0.072417276 -0.01986629  0.04301764 -0.08484861  0.12551261  0.03154033 -0.09408278 -0.02997378 -0.054032625  0.0911418987  0.151438348  0.140147297  0.0839960430 -0.34942241  0.0332716988
KEGG_LYSINE_DEGRADATION                         -0.27646705 -0.27151298 -0.14559260  0.23343969  0.37761951 -0.14982544  0.071650219 -0.03606215 -0.11370614  0.13919560 -0.059279394 -0.148559519 -0.055897641 -0.004205009 -0.084549331 -0.125562528 -0.038538048 -0.095318136 -0.053812331  0.06965729  0.21281299  0.081810273 -0.18178297  0.22842373  0.26345436  0.22182994  0.31463356 -0.21013663 -0.18109835 -0.054938949  0.0360631509  0.177937829 -0.061732716  0.0873730291 -0.14374132 -0.0235819496
KEGG_ARGININE_AND_PROLINE_METABOLISM            -0.16123111 -0.13057226 -0.11107844  0.02273494  0.21356398 -0.07436990  0.084384101 -0.16407155 -0.25289315  0.14391482  0.036172848 -0.326582857  0.055461961  0.147752762  0.096612753 -0.119843646 -0.098278801 -0.122948974 -0.211625005  0.19972609  0.33443209  0.139927393 -0.24553021  0.20165627  0.28074920  0.22470401  0.20124083 -0.21576039 -0.19741636 -0.022915154 -0.0511405637  0.032249241 -0.025522833  0.1225511902 -0.02111686  0.0150635951
KEGG_HISTIDINE_METABOLISM                       -0.38691525 -0.08953562 -0.10044464 -0.01426187  0.01496539 -0.13622135  0.073354885 -0.08532239 -0.06721292 -0.02768174  0.076490066 -0.047484587  0.166533226  0.046557442  0.088751653  0.005292349 -0.081057843  0.067987559 -0.094320047  0.21609906  0.44120825 -0.100792083  0.13452155  0.08461381 -0.02486270  0.31367516  0.26079310 -0.32426284  0.10030542 -0.211640562 -0.0433522226  0.176759090 -0.192709853  0.0459120461 -0.22119461 -0.0645469418
KEGG_TYROSINE_METABOLISM                        -0.32712829 -0.42822607 -0.12167600  0.02926148  0.09223972 -0.04442842  0.021231012  0.02765216 -0.03822786  0.04965165  0.123045871 -0.128743087  0.217063631 -0.020137764 -0.074664972 -0.110309150  0.009697748 -0.014759694 -0.068874216  0.21673625  0.25233361 -0.119479733 -0.10033969  0.17709985  0.13429743  0.33966951  0.19420105 -0.33874057 -0.09490785 -0.124655343  0.1026505643  0.260903234 -0.098142875  0.0001200643 -0.07224524  0.0778319820
KEGG_PHENYLALANINE_METABOLISM                    0.40967474  0.19836523  0.08736858  0.02869842 -0.01374240 -0.09317232  0.234731915 -0.10208931 -0.02436911 -0.04192146  0.046894702 -0.010923766  0.047580560  0.042336433  0.092609398 -0.004019050 -0.309686433 -0.136083760  0.434626863 -0.10463787 -0.38590280 -0.094165597  0.21855328 -0.17952300 -0.11488955 -0.05718921 -0.22158783 -0.01384747  0.01198482 -0.007884161 -0.0977790774  0.182631715  0.047187141  0.0992475649 -0.03286374 -0.1362134528
KEGG_TRYPTOPHAN_METABOLISM                       0.15935872  0.31858549  0.09156412 -0.23847420 -0.09302019  0.08275092 -0.025728297  0.07322292  0.19026430 -0.13868036  0.206619445  0.128988091 -0.078007790  0.096592856  0.011962634 -0.051351485 -0.180762468  0.061269834  0.238903090 -0.09208227 -0.10207168 -0.106243834  0.06774698 -0.08751554 -0.26540552 -0.25036631 -0.51241085  0.26365030  0.06499509  0.024424527  0.0203047444 -0.027556007  0.180543189 -0.0780303726  0.07999529 -0.0340353504
> pickrellPar <- plageParam(pickrellCountsArgonneCQNcommon_eset,
+                          canonicalC2BroadSets, minSize=5, maxSize=500)
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esrnaseq[seq.int(min(nRowsToPrint, nrow(esrnaseq))),])
                                                    NA19099     NA18523       NA19144     NA19137     NA18861     NA19116     NA19130     NA19131    NA19119     NA19152     NA19153       NA19140       NA19138     NA18522       NA19192    NA19193       NA19239       NA19238       NA19210      NA19201     NA19172     NA18870       NA18858     NA18852     NA19159     NA18855     NA19204    NA18501     NA19127      NA19098    NA19093     NA18856     NA18912    NA18517      NA18502       NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                 -0.15214812  0.19079795  0.0106548721 -0.06539635 -0.11195287 -0.04362555 -0.31151529 -0.07757363  0.4492669 -0.18037776  0.04612305 -0.0300515212  0.0095461535 -0.17685565  0.0346814651  0.2305611 -0.0811595896  2.228039e-02 -0.0263523574 -0.003290343 -0.17154720  0.13948803  0.0247698576  0.13773137  0.13227548  0.14302214 -0.11441695  0.3020346  0.07079582 -0.052860583 -0.4212291  0.15020276  0.16979426 -0.1934081  0.003119229 -0.0533843888
KEGG_CITRATE_CYCLE_TCA_CYCLE                     0.15203505 -0.17111274  0.0192425535  0.05927134  0.10807196  0.11312140  0.28808722  0.12139802 -0.4880436  0.15299104 -0.04906447 -0.0147576258  0.0316875534  0.11937406  0.0089518864 -0.2637738  0.0406273352 -4.893202e-02  0.0399987391  0.020132090  0.24689245 -0.14284022  0.0008861416 -0.16483674 -0.08846222 -0.14421236  0.18663124 -0.3056940 -0.10053188  0.025582990  0.2761436 -0.11072658 -0.17974086  0.2615204  0.021548560 -0.0214665332
KEGG_PENTOSE_PHOSPHATE_PATHWAY                  -0.15765014  0.18674949 -0.0273930657 -0.07307133 -0.10533768 -0.09164663 -0.32248478 -0.11596237  0.4765833 -0.14616308  0.04285343 -0.0546959513 -0.0078616045 -0.15559699  0.0056289676  0.2402897 -0.0654167765  9.649199e-03 -0.0248954667  0.014836184 -0.19279004  0.15939724  0.0142917986  0.15493177  0.12077530  0.12820289 -0.13375282  0.3157634  0.06478541 -0.032853560 -0.3012578  0.15637181  0.18509625 -0.2567167  0.011332850 -0.0219922268
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS   -0.09948024  0.17081884  0.0007132175  0.03385509 -0.06241216 -0.10503442 -0.20057306 -0.07219669  0.3963326 -0.12678766  0.06517810  0.0224058492  0.0671487290 -0.18608845  0.0013261299  0.2291769 -0.0210756261  2.665083e-02 -0.0991881059 -0.005604071 -0.49238630  0.15844499  0.0684573628  0.18159133  0.06988761  0.19261084 -0.14240752  0.2382392  0.02679420 -0.052668574 -0.3419867  0.13615421  0.10134608 -0.2093921 -0.007625566  0.0377750733
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM             0.11684514 -0.15932375  0.0424584303  0.08863850  0.01606414  0.07687084  0.26942124  0.09040454 -0.4770715  0.19043992 -0.02814712  0.0084783419  0.0113907130  0.11293532  0.0081665138 -0.2110960  0.0520711362  5.324071e-05  0.0002572043  0.004341436  0.20787937 -0.14010382 -0.0237929613 -0.14074488 -0.11101353 -0.11615857  0.13347359 -0.3440427 -0.08201004  0.014824329  0.4008495 -0.13645213 -0.18798271  0.2656192  0.001164264  0.0452927563
KEGG_GALACTOSE_METABOLISM                       -0.10572541  0.20093414 -0.0337689448 -0.06828622 -0.05141289 -0.04603842 -0.27803249 -0.08715881  0.4593304 -0.16948100  0.02158359 -0.0228842754 -0.0251350377 -0.13562816 -0.0336397673  0.2240697 -0.0559377116  3.578987e-02 -0.0187799930 -0.009111103 -0.19168860  0.14544677  0.0582003469  0.14876379  0.04249027  0.08803668 -0.15131539  0.3368992  0.07977192 -0.004153293 -0.4096545  0.16989169  0.19432462 -0.2523470  0.001213619 -0.0565674873
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM          -0.18741437  0.16387617 -0.0060310939 -0.03859070 -0.14802565 -0.06396724 -0.33253815 -0.09961008  0.4362764 -0.27301158  0.09626864  0.0270197462  0.0232057101 -0.31223804  0.0187798020  0.2361106 -0.0726098042 -4.028766e-03 -0.0969205827  0.054098119 -0.09624125  0.17262148  0.0381393930  0.13351280  0.05969382  0.20522582 -0.04629863  0.2630025  0.13133577 -0.077179005 -0.3109268  0.07680757  0.15756403 -0.1319563  0.004626489 -0.0005768344
KEGG_FATTY_ACID_METABOLISM                       0.14404628 -0.17549826 -0.0168733006  0.03662427  0.13805007  0.13510632  0.29212490  0.11769787 -0.4538781  0.16997502 -0.05292794 -0.0171357447  0.0056091986  0.20068593 -0.0171192068 -0.2391582  0.0523800221 -3.355725e-02 -0.0037541309  0.007606301  0.26720390 -0.13680786 -0.0229006319 -0.12955701 -0.16649337 -0.18843753  0.11227260 -0.3030089 -0.07180728  0.065746889  0.3537898 -0.09725041 -0.16000999  0.1584219  0.002131614  0.0267022633
KEGG_STEROID_BIOSYNTHESIS                       -0.23993046  0.13867049  0.1187377626  0.05110320 -0.13720084 -0.17477296 -0.20358441 -0.12237759  0.4362713 -0.01023068  0.09255610  0.0831711016 -0.0316845885 -0.09055792 -0.0101667462  0.2066797  0.0664619590  6.476799e-02  0.0581287322  0.001741120 -0.22245981  0.14966908 -0.0538040397  0.16575480 -0.03806247  0.08839711 -0.09754098  0.3146994  0.09568740 -0.024727977 -0.3582404  0.08721987  0.08303645 -0.3500921 -0.182876427  0.0455568716
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS             -0.10378950  0.13345241  0.0602863571 -0.16623904 -0.07063215  0.01365008 -0.19534754 -0.17435286  0.4708230 -0.07118342  0.11618557 -0.0502633451 -0.0554177755 -0.16614665  0.0076810221  0.2090015  0.0672454536  3.512318e-02 -0.0428960078 -0.024698829 -0.33368337  0.14917398  0.0139906079  0.08658955  0.10773984  0.14806389 -0.11894824  0.3430318 -0.01837218 -0.088410625 -0.4130314  0.11951559  0.13746845 -0.1309977 -0.048676576  0.0540649156
KEGG_STEROID_HORMONE_BIOSYNTHESIS               -0.21197941  0.18630856  0.0301018384 -0.11630509 -0.04474517 -0.08691530 -0.11027761 -0.11733030  0.4409750 -0.20162476  0.13665328  0.0221236331 -0.0003285179 -0.14428211  0.0620844698  0.1180512  0.0562025241  1.740092e-01 -0.0893062456  0.018200638 -0.29453200  0.08782095  0.0795061796  0.14770804 -0.04685136  0.10482351 -0.13782587  0.3286641 -0.01216641  0.001473664 -0.4633424  0.07796440  0.16692838 -0.1512924 -0.030595788  0.0201011702
KEGG_OXIDATIVE_PHOSPHORYLATION                   0.11392670 -0.15176080 -0.0078716193  0.03185503  0.08755261  0.16899727  0.27816007  0.10828366 -0.4984539  0.15443204 -0.05388480 -0.0005382922  0.0143975861  0.13323583 -0.0144179595 -0.1631206 -0.0012127107 -4.539461e-02  0.0435086752  0.022640863  0.29947218 -0.13776551 -0.0302126129 -0.18067891 -0.13765087 -0.16335643  0.12104839 -0.3312689  0.02163840  0.030604155  0.3449082 -0.11292053 -0.11048607  0.2310232 -0.025202957 -0.0394868208
KEGG_PURINE_METABOLISM                           0.14576228 -0.17970119  0.0695643645  0.07390013  0.09426888  0.14811626  0.25313045  0.12971197 -0.4997313  0.16664358 -0.06909949 -0.0011720262 -0.0279803304  0.13994248  0.0019350762 -0.1746847  0.0245422008 -6.364770e-02  0.0941657279  0.013648424  0.26762396 -0.16851615 -0.0456918476 -0.19287243 -0.08967612 -0.14275219  0.16046531 -0.3211839 -0.02696631  0.051340413  0.2707759 -0.12761083 -0.17070100  0.2401788 -0.012335268 -0.0313934410
KEGG_PYRIMIDINE_METABOLISM                      -0.15527782  0.18681216 -0.0710134938 -0.09272258 -0.09107116 -0.15945406 -0.26422713 -0.13051958  0.4924685 -0.17590868  0.06869025  0.0017294883  0.0440173962 -0.15137425 -0.0069782437  0.1818896 -0.0252424604  5.910549e-02 -0.0641390004 -0.009211103 -0.25500824  0.17506163  0.0368705159  0.19122864  0.11892819  0.15054298 -0.17164591  0.3047345  0.02982096 -0.059310144 -0.2438609  0.10353402  0.16710577 -0.2540935  0.041640375  0.0268777463
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM  0.16187518 -0.15242447  0.0445845851  0.03801959  0.16815027  0.15816036  0.18629258  0.13647099 -0.4547896  0.15764760 -0.09834758 -0.0673653703 -0.0327515803  0.13813612 -0.0001154741 -0.2242866 -0.0035237558 -8.144324e-02  0.0846143930  0.016951778  0.35755319 -0.12650621 -0.0869564600 -0.15472376 -0.13565892 -0.15047719  0.19304761 -0.2923463 -0.10340182  0.124156397  0.2929275 -0.08529239 -0.17347808  0.1458381  0.019564617 -0.0001020227
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM     0.18425567 -0.21997777  0.0792549975  0.02796617  0.15066508  0.13108206  0.09096202  0.09603363 -0.4087696  0.19271142 -0.11346497 -0.0412294265 -0.0825276719  0.25407808 -0.0336109990 -0.1920607 -0.0511250493 -1.385250e-01  0.0965515196 -0.005825203  0.28983157 -0.12541010 -0.0631413865 -0.18063408  0.07210946 -0.15207612  0.12502562 -0.3434555 -0.08266163  0.241050135  0.2367705 -0.13650734 -0.16052837  0.1219852  0.122337569  0.0188602175
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM          0.21582742 -0.19257267  0.0481026570  0.12532384  0.12863263  0.12702487  0.21916790  0.14145654 -0.4628510  0.18903573 -0.08990904 -0.0356654022 -0.0293211714  0.21616290  0.0113339421 -0.2359683  0.0240081539 -8.452455e-02  0.0615230196 -0.031731840  0.26949610 -0.14960573 -0.0490440852 -0.18626782 -0.06807870 -0.13588057  0.13260775 -0.3153507 -0.07004173  0.095123437  0.2314867 -0.12190522 -0.17317799  0.1942247  0.001740289 -0.0003819966
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION  -0.13320980  0.19146649  0.0001692046 -0.04724794 -0.11203115 -0.10900765 -0.32384751 -0.08670029  0.4661106 -0.15194445  0.02163166  0.0263972205 -0.0156839833 -0.23372426  0.0016790308  0.2330446 -0.0339518900  2.867854e-02 -0.0347112069 -0.013832614 -0.26086893  0.15508615  0.0463970898  0.12786410  0.13562535  0.16840661 -0.11800503  0.3056234  0.08931534 -0.062290601 -0.3304639  0.11023004  0.15287141 -0.1761863 -0.010338119 -0.0065512747
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS -0.18497233  0.17649821  0.0506236410 -0.08746720 -0.15678895 -0.18326441 -0.19998683 -0.08831954  0.4498416 -0.09855080  0.04904952  0.0387063020  0.0391040897 -0.19473731 -0.0088725559  0.2294151 -0.0153974275  8.110413e-02 -0.0361551097 -0.038686397 -0.29902619  0.15638790  0.0813030069  0.15365219  0.07778971  0.14702327 -0.22562370  0.2961998  0.06095390 -0.060339944 -0.3294075  0.14871582  0.15615268 -0.1661644 -0.018031872 -0.0007282847
KEGG_LYSINE_DEGRADATION                         -0.14840078  0.19887266 -0.0896794806 -0.05874662 -0.09522200 -0.16067588 -0.25024857 -0.12714531  0.5089357 -0.17188541  0.06501566  0.0211715670 -0.0087000106 -0.11468731 -0.0192207645  0.1887464 -0.0086852919  9.220565e-02 -0.0997662839 -0.015545295 -0.25889646  0.14938001  0.0102360429  0.15953226  0.08245914  0.11756512 -0.12447080  0.3428059  0.05803155 -0.041416622 -0.2706288  0.11974209  0.19925355 -0.2252852 -0.018670642 -0.0059757956
KEGG_ARGININE_AND_PROLINE_METABOLISM            -0.15599441  0.17162854 -0.0165755907 -0.04984281 -0.13252570 -0.13503025 -0.24149898 -0.12496608  0.4652361 -0.18264708  0.06245441  0.0533993450  0.0200002688 -0.17588537  0.0187300201  0.2268855 -0.0308582433  6.457058e-02 -0.0409831672 -0.022302704 -0.26703092  0.13286020  0.0597241639  0.15221801  0.12299299  0.13822870 -0.16751098  0.3220956  0.08792924 -0.097087427 -0.3352892  0.08674901  0.18213748 -0.1854224 -0.015128027  0.0087392720
KEGG_HISTIDINE_METABOLISM                       -0.16341627  0.21211137 -0.0597047650 -0.07019812 -0.06569836 -0.16907760 -0.24238369 -0.09397806  0.4720904 -0.22248144  0.09449529  0.0337872241  0.0814929382 -0.14765066  0.0166344423  0.1896539 -0.0151032687  7.080535e-02 -0.0387446192 -0.034208862 -0.28356932  0.13501819  0.0592272252  0.14530433  0.09060491  0.16483382 -0.08830364  0.3105553  0.03130984 -0.076375024 -0.3379780  0.10320490  0.12281655 -0.2312373 -0.020753794  0.0269168631
KEGG_TYROSINE_METABOLISM                        -0.10093863  0.18267763 -0.0242538303 -0.06443060 -0.02632197 -0.16928691 -0.21835995 -0.12802624  0.4897721 -0.20718144  0.08915284  0.0230208339  0.0685731978 -0.11497401  0.0264683523  0.1715784 -0.0240623350  5.461238e-02 -0.0359349395 -0.041186627 -0.34571344  0.11565207  0.0429404806  0.15350966  0.12352853  0.16156040 -0.14241499  0.3437890 -0.02098569 -0.034677062 -0.3320536  0.12420589  0.08212171 -0.1959923 -0.039814920  0.0134459864
KEGG_PHENYLALANINE_METABOLISM                   -0.13596282  0.06742145  0.0882449903 -0.02244406 -0.09867622 -0.06439912 -0.08447981 -0.15306648  0.4203738 -0.10031185  0.17368849  0.0780588540  0.0996577430 -0.02544390  0.0171562407  0.1211227  0.0235791297  8.347408e-02 -0.2466780511 -0.006247915 -0.61710863  0.07252436  0.0317753835  0.10302349  0.06683344  0.11139551 -0.15093291  0.2664307  0.04334024 -0.011422551 -0.1744265  0.11107338  0.02648540 -0.2152238  0.019167613  0.0819975622
KEGG_TRYPTOPHAN_METABOLISM                       0.17049240 -0.19170650  0.0004630847  0.05089247  0.12593277  0.11515466  0.27670376  0.12909756 -0.4814202  0.17977370 -0.06320424 -0.0194461931  0.0070929693  0.19100894 -0.0230060896 -0.2042648 -0.0001048516 -7.878183e-02  0.0931404987 -0.026808640  0.24465868 -0.13838085 -0.0248749524 -0.16243909 -0.09741608 -0.15878157  0.07600539 -0.2897865 -0.09352519  0.056621625  0.3530154 -0.08401918 -0.15938269  0.2105366  0.043211634 -0.0264526019
> 
> gbmPar <- plageParam(gbm_eset, brainTxDbSets)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
                    TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up               0.009503434         -0.07148275          0.03702570          -0.1449671         -0.06040476         -0.07594821         -0.08471232        -0.011938741          0.02993423         0.065023141          0.01762836         -0.11912551         -0.05949992          0.00525537         -0.05523948         -0.05372246         -0.08443369         -0.08598174         -0.11875051        -0.042058976         -0.04030687        -0.085476621         -0.10685594          0.02611153          0.04356317       -0.0705649980        -0.006844708         -0.01728745         -0.05473265         -0.02670516        -0.023271397         0.028072017         -0.03921781         -0.10235048         -0.05010187         -0.07005158         -0.09209016         -0.10881587         -0.05062336        -0.007877207         -0.08243841         -0.06962198         -0.08767648         -0.02583498         -0.04666987         -0.07810986         -0.01152421          0.02981450         -0.08655273        -0.024763415
astroglia_up                0.047878697          0.13259958          0.09353196           0.1723954          0.05397369          0.09437815          0.12333017         0.034441261         -0.02691552         0.082648790          0.05525398          0.07854437          0.02675066          0.14436470          0.03635936          0.07445693          0.18500914          0.12978579          0.10685532        -0.046038185          0.03640657         0.134998687          0.14571431          0.16997016          0.02481540        0.0363660300        -0.020974725          0.08501924          0.13807016          0.11677809        -0.008999474        -0.020349973          0.05204384          0.04461865          0.09432334          0.05564952          0.05441292          0.07187041          0.06496384        -0.016408375          0.06458610          0.08187014          0.14767961         -0.01197801          0.03687600          0.06445718          0.01797752          0.01595298          0.09244863         0.052499964
neuronal_up                -0.109710924         -0.01702066          0.01301810          -0.0150155         -0.09724660          0.02146057          0.05010519        -0.040146081         -0.06066290        -0.006770987         -0.11536936          0.07187279          0.06404673          0.05934842          0.01706701          0.06703005         -0.05028874          0.06844218          0.03520158        -0.007305407         -0.02100709        -0.009551983         -0.02286479          0.02104686          0.02714991        0.0009992218        -0.091286596          0.04988690          0.05224805          0.04092799        -0.012195643         0.009698397         -0.03329177         -0.03730078         -0.06501777          0.00777109         -0.01276343         -0.07101898         -0.03167425         0.008950496         -0.04525475          0.03152291         -0.05007149         -0.06206634          0.00277177          0.05362907          0.06015409         -0.12476908          0.01965553        -0.006541254
oligodendrocytic_up        -0.053316262         -0.03076570         -0.13026183          -0.1054244         -0.15884604         -0.04584733          0.01162552        -0.008735686         -0.07831724         0.029790216         -0.12264757         -0.17633055         -0.22829418         -0.09563053          0.01913198         -0.08062237          0.06710752         -0.04973426         -0.09459566        -0.035043759         -0.07087794        -0.024834220         -0.14132943         -0.08015759         -0.12351419       -0.1018570138        -0.145485987         -0.08031675         -0.13791221         -0.06314112        -0.055013638        -0.111969729         -0.06278656         -0.12395121         -0.11149668         -0.13560637         -0.03100847         -0.11540779         -0.19569986        -0.004032233         -0.09848717         -0.01310448         -0.01601479         -0.08806238         -0.15998008         -0.03256551         -0.02666356         -0.04873438         -0.04271502        -0.015764935
                    TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up               -0.10887523         -0.07864038         -0.04197239         0.095668384          0.18776408          0.25307779          0.08792407          0.05994647          0.13261591         0.021215334           0.1151069          0.12610727          0.11787216          0.03692715          0.07098464          0.06193001          0.05640898          0.07437529          0.03446988          0.13673871          0.05740561          0.04951662         -0.03940410          0.07655210          0.08887779          0.06360155         0.063447530          0.09165828          0.10386274         0.098671883          0.08994742          0.14845583          0.05137301         0.101763991        0.0439691905          0.12523626         -0.05949182         -0.02266147          0.04146871         -0.01734481          0.02456185        -0.005848951          0.11898178        -0.003748745          0.04014935         0.049498323        0.0378446673         0.028926994         0.081286268          0.06431596
astroglia_up                 0.13560615          0.06372746          0.09853784        -0.061051452          0.01577089         -0.04760733         -0.01301234         -0.02033879          0.03042881         0.007860558           0.1302317          0.04866147          0.11807311          0.02651416         -0.02576869         -0.02249800          0.03139450          0.01262743          0.10298674          0.04376961         -0.02441912          0.04007613          0.10426429          0.05984316          0.09531040          0.01361742        -0.006054302          0.01417130          0.01785855        -0.024485729          0.04885270          0.04978712          0.01089287        -0.003688539       -0.0255875216         -0.05318817          0.01572855         -0.04017804         -0.01581070          0.08027547          0.06475093        -0.019267885         -0.01000033        -0.012468882          0.03808888         0.016444129        0.0004891894         0.006058522         0.001277776          0.04623002
neuronal_up                 -0.01603674          0.03026768         -0.04846411        -0.081274578          0.03036729         -0.10588657         -0.04819897         -0.21472580         -0.07924660        -0.014852256          -0.3937604         -0.10090691         -0.42227945         -0.02226663         -0.03522747         -0.15937196          0.02880150         -0.03360695         -0.19537945         -0.02678998         -0.01237703         -0.05800257         -0.08946093          0.02804959         -0.33447989         -0.06646701         0.001490673         -0.06111592         -0.00788255        -0.005433944          0.08875419         -0.04552211          0.06832540        -0.054242676       -0.0165587308          0.03709143          0.08683758          0.07694510          0.00983925          0.05086959          0.03951686         0.046397028          0.03379387         0.065956603          0.07285765         0.002567756        0.0022974121         0.076873274         0.040563891         -0.04577361
oligodendrocytic_up         -0.09082646         -0.03209598         -0.06775336        -0.001343057          0.09570037         -0.04469363         -0.03506036         -0.09033811          0.01079102        -0.008493560          -0.1060987          0.02222565         -0.09131953         -0.02902642         -0.01525947         -0.07435504          0.08049313          0.05654690          0.03601434          0.01580467         -0.08981765         -0.01162585          0.03884722         -0.00640505         -0.11088869          0.06651459         0.048149691          0.05667692          0.06740432         0.057691526          0.05627159          0.01676310          0.06553035         0.068221314        0.0005776113         -0.02757186          0.07961760          0.03639202          0.08426877          0.07545897          0.07456736         0.040406936          0.06787397         0.080378144          0.05427988         0.059627054        0.0040825991         0.039001591         0.038807887          0.01393330
                    TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up                0.10254985        0.1209366458         0.005457102          0.05470414          0.05324132         0.004583494          0.07287897          0.01803334         0.092298928         0.106581126          0.03911847          0.08760433          0.08083304          0.12273304          0.08658859          0.09439140          0.12859993          0.12899656         -0.05799326         0.043791271         -0.12734557         -0.07620178        -0.101627927          0.07398850         -0.14128439          0.04168816         -0.10586947         -0.07738761         -0.05189054         -0.04129260        -0.029881354         -0.02425999         -0.03083819         -0.01363261         -0.03413866          0.03369514         -0.02533095        -0.026089207         -0.05887989        -0.023565388         -0.02660048         -0.13175535        -0.131223466         -0.04934655         -0.07222247          0.04595771        -0.002484733         -0.02006267         -0.02129216        0.0121870804
astroglia_up                 0.01473182       -0.0002823507        -0.041514372         -0.04221281          0.05781689         0.010362305         -0.03948686         -0.02292038         0.009218869         0.003819796          0.08805820          0.05787047         -0.04832227         -0.04771188         -0.03770525         -0.00397720          0.01702062         -0.04901255         -0.15053965        -0.066808334         -0.12029138         -0.13543562        -0.111383004         -0.11055588         -0.07080332         -0.05626645         -0.16040451         -0.06003255         -0.11320734         -0.07762499        -0.067457036         -0.06885981         -0.07206253         -0.09501078         -0.08210609         -0.14076913         -0.09259525         0.017705647         -0.07440865        -0.075879552         -0.10686648         -0.12383580        -0.109491916         -0.05092156         -0.12756381         -0.04676953         0.016467894         -0.08296504         -0.11449864       -0.0624475003
neuronal_up                 -0.05510838        0.0693924418         0.049907805          0.06579639         -0.03553495         0.060569667          0.04258533          0.05347991         0.011061722        -0.022561037          0.05657129          0.08324986         -0.06484210          0.05410708          0.08696189          0.04328396          0.04756120          0.05241028          0.03859840         0.004121992          0.05429824          0.06696186         0.039995573         -0.03731216          0.03871302          0.01346663         -0.02003846          0.03361013          0.08956373          0.05912840         0.004434217         -0.12181570          0.03493980          0.01353410          0.04421769          0.01083988          0.03740344        -0.008455138          0.03989240         0.043233261          0.03530835          0.04811405         0.067893057          0.06035066          0.05073357          0.04311893         0.074185702          0.05368352          0.04001603       -0.0368438811
oligodendrocytic_up          0.01488734        0.0588328752         0.073964840          0.05639762          0.06448371         0.103919757          0.05028910          0.07722783         0.094043741         0.035205083          0.07003096          0.06202171          0.04362975          0.05582357          0.08811635          0.07662414          0.06354034         -0.13317556          0.09801811         0.010237076          0.04782735          0.09917287         0.003572068          0.02818885          0.12062411          0.06959310          0.09380954          0.09824244          0.04046508          0.05673212        -0.016644605         -0.11809801          0.06714657          0.02817944          0.07503049         -0.01017455         -0.01208933        -0.031760653         -0.16273288         0.008979194          0.06577860          0.08468706         0.006857635         -0.03150528         -0.03036885          0.08254308         0.070749406          0.09400074         -0.01657986       -0.0003181655
                    TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up               -0.12793182          0.05813961         -0.02996638         -0.03999179         -0.01317216         -0.06556770         -0.06014645         -0.10524550          0.03410507          0.03174620         -0.07131517         -0.03864651         -0.00656357         0.004862977         -0.05760770         -0.03220225         -0.14379979         0.006209294          0.01015281         -0.02506194         -0.15712941         -0.06978470        -0.039842096
astroglia_up                -0.07509997         -0.03112873         -0.07460949         -0.10572792         -0.07367029         -0.08467325         -0.05192066         -0.04367356         -0.07272862         -0.06252615         -0.10738803         -0.07352765         -0.08211912        -0.086061829         -0.11834540         -0.05541622         -0.05335162        -0.071461495         -0.06913880         -0.14663735         -0.10229018         -0.04606975        -0.030543430
neuronal_up                  0.04965757          0.03625217          0.04174849          0.04119978          0.04325152          0.04343971          0.04604542          0.03545067          0.04582293          0.07345420          0.01598958         -0.00251816          0.03897229        -0.071738618          0.06571136         -0.05706466          0.03314141        -0.016854947          0.07308937          0.04576623          0.03139639          0.06476292         0.047577132
oligodendrocytic_up          0.06265322         -0.03057294          0.08799201          0.04420027          0.07389345          0.10096870          0.02276466          0.04904987          0.08861485          0.09026904          0.06005119          0.02120084         -0.02586168         0.056221418          0.04705479          0.02053537          0.11599128         0.059425833          0.04519846          0.09306496          0.10243557          0.07848995         0.009634767
> 
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+                                 grep("_DN$", names(c2BroadSets)))]
> leukPar <- plageParam(leukemia_eset, cgpC2BroadSets,
+                      minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
                                                  CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP                    -0.1733940255       -0.033909950        -0.21494771        0.225895163        0.063750234        0.167895761       -0.120141623       -0.301364574       -0.127897961        -0.17662816      -2.033307e-03      -0.0580768131         0.22143221        -0.10332109        -0.22150927        0.043353690        -0.25639842        -0.09207537        -0.08853224        0.026931498        -0.14639547        0.099528895      -0.0728970131         0.20132393        0.071949059        0.065447939         0.14428259        0.131615034        -0.13550381        0.058275958         0.32869002         0.11720023        0.110313219       1.576915e-01         0.36374728       -0.052301552       -0.221995813
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP                    0.0091056904       -0.007229294        -0.26682324        0.239296160        0.102079970        0.107282626       -0.220934366       -0.114993916       -0.242707246        -0.35282402      -1.319142e-01      -0.2908596517         0.19217905        -0.05096841        -0.30028124        0.081213713        -0.06235553        -0.03413274         0.14630064        0.233615255        -0.02563993        0.216233541       0.1512191200         0.18209821        0.096718310        0.012136911         0.05625600        0.144054943         0.15035428       -0.046779826        -0.05975187        -0.23316425       -0.056470909      -4.192709e-02         0.16251868        0.109530419        0.147564140
WINTER_HYPOXIA_UP                                       0.0834055313       -0.070653851         0.36411795       -0.247095973       -0.178229854       -0.221082475       -0.024371138        0.180921942        0.038462365         0.10271188      -6.399298e-02      -0.0082717873        -0.01821576         0.28000441         0.17834176       -0.050337001         0.11095592         0.07805238         0.10651755       -0.242836351         0.23470420        0.062017426       0.0444107834        -0.26140415        0.191019536        0.057727131        -0.25471951        0.003543483         0.20328048        0.027252717        -0.16090502        -0.15356573       -0.065566664       5.311727e-02        -0.35349585       -0.060628683        0.034808040
PYEON_HPV_POSITIVE_TUMORS_UP                           -0.1194662949        0.038017996        -0.28521866        0.275081686       -0.031488732       -0.038588970       -0.100533814       -0.297050611       -0.238634457        -0.29082863      -7.600985e-02      -0.2335338233         0.31515092        -0.08353618        -0.18336902        0.087151767        -0.20372452        -0.14291385         0.03273765        0.233092544        -0.04825298        0.113859039       0.0442618489         0.16991714        0.231386554        0.005267212         0.03397312        0.099018174        -0.04752945        0.167145951         0.12918791        -0.11535230        0.055991634       8.848689e-02         0.24812128        0.117475851        0.050707009
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP            0.1198739462        0.187824071         0.39422522       -0.345600421       -0.152731606       -0.106308076        0.142740956        0.120710037        0.111680385         0.07724317      -8.733673e-03       0.0899926339        -0.06187972         0.35041893         0.14911728       -0.027779682         0.08478613         0.05561965         0.01558144       -0.248802758         0.23046261        0.041120203      -0.0006047729        -0.26801992       -0.003634823        0.026561742        -0.21188895       -0.043144995         0.07637875       -0.133457745         0.15331729        -0.05186474       -0.076486263      -1.260192e-01        -0.25406257       -0.154880107       -0.151754404
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP                0.2252138709       -0.016371911         0.37845026       -0.211838619       -0.067003022       -0.082541632        0.107463748        0.354471664        0.050713686         0.05482788       3.898683e-02       0.0381826905        -0.26206483         0.04681314         0.14091476        0.033986348         0.26834682         0.12993489         0.11032619       -0.004324969         0.16729155       -0.004938875       0.0658737109        -0.21012140       -0.044233735       -0.047256310        -0.15738147       -0.115751643         0.13986387       -0.054860717        -0.29955088        -0.13555352       -0.170517674      -1.622639e-01        -0.29957850       -0.092711253        0.087202988
LU_TUMOR_VASCULATURE_UP                                -0.2378969459       -0.062771846        -0.34031239        0.168539328       -0.005657595        0.008190157       -0.167323313       -0.338981975       -0.012484156        -0.02906254       7.237425e-02      -0.0041181720         0.05644821        -0.09547833        -0.17278295       -0.026587364        -0.15721892        -0.08290324        -0.07692133        0.027096635        -0.15539443       -0.039807725      -0.0907044859         0.15741811        0.099085419       -0.025321125         0.12258506        0.194526161        -0.21552019        0.417930079         0.09449431         0.15446705        0.179506032       2.947411e-01         0.20435875        0.153196747       -0.067708347
KORKOLA_EMBRYONAL_CARCINOMA_UP                         -0.0648890101       -0.032521742        -0.09549351        0.129393718       -0.193203052        0.019756674        0.033055489        0.012090742        0.162133586         0.15343460       5.965502e-02      -0.0946327900        -0.14723402         0.14926621         0.08055377       -0.069317678         0.09878785         0.05716404         0.27551849        0.032230796        -0.22770260       -0.151166173      -0.2096628767        -0.10471736        0.361843632       -0.171443414        -0.17937880       -0.066953233         0.01485418        0.028228846        -0.09265788        -0.07985186       -0.145152990       5.837802e-01        -0.10747460       -0.064683118        0.046388878
KORKOLA_TERATOMA_UP                                     0.0246879829        0.314207438         0.37605979       -0.179124841       -0.032379168        0.129238282        0.172225286        0.235548971       -0.014739292         0.16769097       1.663879e-01       0.0188106200        -0.04650602         0.01986651         0.08451226       -0.166920945         0.17295139         0.03802788         0.12813343        0.126220125        -0.18602937       -0.161481817      -0.1742658425        -0.24643129       -0.122836999       -0.327714071        -0.29192403       -0.145207142        -0.09418954        0.059783879         0.09598647        -0.03320679        0.003223224      -1.181121e-01        -0.17877126        0.090599349        0.095678786
KORKOLA_YOLK_SAC_TUMOR_UP                              -0.0007555054       -0.021421796         0.02632694       -0.035433567        0.141613226        0.019911372       -0.004796058       -0.001649931       -0.102005325        -0.05763990       3.689459e-05       0.1935898594         0.20317659        -0.19638421        -0.08784612        0.042714637        -0.07671928         0.02373285        -0.34386769        0.028515433         0.18531115        0.075685824       0.1123704848         0.11078104       -0.341628831        0.120190881         0.08150623        0.099416803        -0.10395047       -0.040783114         0.10255693         0.11340823        0.112870194      -6.356078e-01         0.19628606        0.082304700       -0.021816705
KORKOLA_CHORIOCARCINOMA_UP                              0.1041128574        0.050802605         0.08356868        0.002616351        0.166705865        0.029083321        0.033339356        0.034863888       -0.145879153        -0.07857234      -1.949332e-02       0.1514434265         0.20246406        -0.23759405        -0.08452061        0.043151694        -0.08551227        -0.03830657        -0.31848162        0.011160018         0.16614410        0.086788071       0.0890085722         0.08732890       -0.362402733        0.121010372         0.11882511        0.112394298        -0.10527127       -0.045309504         0.09942631         0.07787554        0.114541375      -6.194077e-01         0.15411825        0.063366395       -0.063388257
KORKOLA_SEMINOMA_UP                                     0.0143883280       -0.061538315        -0.07332409       -0.002029272        0.217358315        0.098241098        0.032751796       -0.087814242       -0.081314491        -0.06460506      -5.616862e-03       0.1630969932         0.21820386        -0.21452236        -0.11089417       -0.032477859        -0.09300386         0.04122480        -0.28319229        0.073437921         0.09605443        0.020087468       0.1290883909         0.12890302       -0.381385908        0.084072436         0.16921641        0.055552661        -0.12958319       -0.053707297         0.10910509         0.13519677        0.161922009      -5.578087e-01         0.23735022        0.103641126       -0.056075120
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP       0.1123404419       -0.099246059         0.29251507       -0.325596653       -0.052662019       -0.012940114        0.154217301        0.308497258        0.189224705         0.17168566       1.231780e-01       0.1182710250        -0.19858688         0.12426680         0.23060251       -0.113059070         0.23861910         0.12627316         0.13843072       -0.039936738         0.03939179       -0.122691635      -0.0569411621        -0.14852082       -0.101765053       -0.037504955        -0.13765046       -0.140529751         0.04455761       -0.014788011        -0.25402909        -0.05853212       -0.116016632      -4.783914e-03        -0.41905900       -0.014673495        0.057442498
HOLLMAN_APOPTOSIS_VIA_CD40_UP                          -0.1151565209        0.052711436        -0.29807776        0.247422702        0.147590241        0.055423242       -0.142427543       -0.297218464       -0.186224424        -0.20741716      -1.121865e-01      -0.0760119941         0.24124543        -0.14203473        -0.20234670        0.043247386        -0.27180186        -0.07873619        -0.18050744        0.114991470        -0.02127029        0.167118090       0.0958585482         0.22051043        0.002936958        0.072780412         0.15534893        0.139476566        -0.15101819       -0.017452203         0.18358194         0.10429137        0.142368910      -3.065258e-02         0.33247353        0.112098951       -0.100935977
LIU_PROSTATE_CANCER_UP                                  0.2174486111       -0.073496729         0.28573856       -0.124499192       -0.057239993       -0.020429757        0.140693421        0.407214699        0.120220601         0.12989182       2.508589e-02       0.0967480905        -0.25967413         0.13919891         0.19209378       -0.031730039         0.24893454         0.09710975         0.17247772       -0.030756115        -0.11270677       -0.121554641      -0.0857006060        -0.09446246        0.010098924       -0.184232968        -0.21029038       -0.115727215         0.11745326       -0.045479539        -0.29983687        -0.12332926       -0.224404303      -3.488958e-05        -0.24405810       -0.081462154        0.140697510
LIU_SOX4_TARGETS_UP                                     0.0348520543       -0.161469634         0.26274156       -0.304202295       -0.050685124       -0.053041216        0.085962358        0.301189290        0.166324484         0.13116039       1.100475e-01       0.0647346500        -0.33897362         0.04852868         0.24684466       -0.016577714         0.23365434         0.07455878         0.16613184       -0.016965465         0.02436819       -0.227625669      -0.0004191321        -0.12194013       -0.111578239       -0.041314905        -0.09052165       -0.097587342         0.17721669        0.085952083        -0.28194043        -0.05932238       -0.057205746       5.321372e-02        -0.36367249       -0.015363998        0.142925944
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP          -0.0934159787        0.060976175        -0.26757898        0.202795542        0.127852418        0.116405632       -0.105679519       -0.207537683       -0.127761790        -0.21806297      -8.009341e-02      -0.0570496808         0.35572293        -0.16622240        -0.23033722       -0.003656037        -0.24351471        -0.08281439        -0.21385192        0.089045910         0.05702248        0.162830271       0.1073197522         0.18581478       -0.043297663        0.140169126         0.16915870        0.130244227        -0.19356051       -0.078973917         0.21181563         0.09276215        0.124145090      -2.047438e-01         0.27452947        0.097684909       -0.088142625
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP               -0.2531769445       -0.076391547        -0.35524046        0.178419647       -0.027932256       -0.062111318       -0.190294011       -0.401869438       -0.047034396        -0.09050315      -7.353341e-02      -0.0001531211         0.17442433        -0.05326287        -0.19853240       -0.023615069        -0.28054125        -0.06056164        -0.13689646       -0.006535930        -0.05171414        0.065779649       0.0174894144         0.18666747        0.145560303        0.080587372         0.12046867        0.174873906        -0.04655476        0.182351256         0.20782555         0.13377643        0.169157456       1.914065e-01         0.28928058        0.137016903       -0.018630858
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP               -0.1411454025        0.047900582        -0.25625196        0.269176774        0.181462253        0.034784740       -0.116174263       -0.301870796       -0.044968652        -0.14811820      -8.208908e-02      -0.0352154619         0.29059194        -0.07287436        -0.20680686        0.017363938        -0.30032548        -0.11323896        -0.17005992        0.006601310        -0.06746557        0.077409057       0.0159590455         0.26558390       -0.037694782        0.167440913         0.21207543        0.140875368        -0.19160167       -0.060321378         0.24086742         0.10370036        0.094599476       2.850367e-02         0.28597165        0.029669499       -0.164314548
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP                    0.1116529885        0.292188184         0.34831334       -0.123581722        0.050516147        0.145019714        0.206187041        0.163406743        0.007821523        -0.09940156       4.141215e-02      -0.0228886983        -0.05491470        -0.03095383         0.10860314        0.072183090         0.13099797         0.06711451        -0.07673696        0.041966891         0.25476428        0.177618166      -0.0154400900        -0.13870532       -0.100030138       -0.108760557        -0.10667785       -0.165118186        -0.21136962       -0.308830865         0.01307193        -0.01994302       -0.006007855      -5.126714e-01         0.03798671       -0.170143211        0.001351049
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP                     0.2745402112       -0.044177556         0.31876654       -0.329339068       -0.105691495       -0.142140913       -0.003162191        0.157173800        0.089932849         0.07302904      -1.286126e-02       0.0758662612        -0.43830863         0.10777430         0.12826241        0.012040783         0.27425517         0.11749725         0.05930217        0.038952950         0.07519665       -0.100333208       0.0973981350        -0.10538721       -0.085077261       -0.021507687        -0.12994877       -0.094083007         0.20864101       -0.006430176        -0.19660903        -0.01719751        0.009752194      -1.663727e-01        -0.31852933       -0.004341272        0.203116535
FRASOR_TAMOXIFEN_RESPONSE_UP                            0.2257957178        0.048434395         0.37131451       -0.247543764       -0.045657194        0.045635878        0.177470440        0.343445989        0.118508293         0.14408488       1.239577e-01       0.0438059242        -0.29647471         0.08855053         0.19195553       -0.026278996         0.24448407         0.11560848         0.07867322       -0.017378686         0.01098018       -0.168135671      -0.0825024498        -0.12893972       -0.172576527       -0.076678534        -0.18549006       -0.155205808         0.02425944       -0.011353726        -0.15818606        -0.07181830       -0.088612281      -2.797678e-02        -0.36273060       -0.104253429        0.030828162
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP                  -0.2233367530       -0.007741796        -0.37463807        0.260361044        0.062097031        0.042551473       -0.111730786       -0.361252426       -0.028706282        -0.04328331      -4.884767e-02       0.0149329143         0.25979025        -0.12316554        -0.20828246       -0.016039857        -0.15973390        -0.13573929        -0.06858283        0.107131118        -0.19184527        0.008118677      -0.0431836820         0.18748450        0.078381562        0.029201247         0.23179224        0.070307687        -0.20823179        0.030900475         0.23092058         0.16884357        0.117332432       1.166270e-01         0.32408086        0.047668182       -0.034181119
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP                    0.1108356219        0.072625095         0.35562137       -0.266060947       -0.107490386       -0.048812016        0.183603465        0.203732983        0.195010034         0.30190337       5.026785e-02       0.1833451993        -0.21665967         0.10730554         0.19889431       -0.080954542         0.22126893         0.13154304         0.03614184       -0.220001339         0.11292678       -0.131457134      -0.0455743876        -0.27755754       -0.067880624       -0.016925423        -0.14254500       -0.174080097         0.03526815       -0.091897678        -0.03194165         0.07521659       -0.066452401      -4.426222e-02        -0.30126507       -0.155867534       -0.087824518
WATANABE_COLON_CANCER_MSI_VS_MSS_UP                     0.1604393078       -0.046725031         0.24421714       -0.212744255       -0.088335734       -0.062050470        0.127640749        0.301282112        0.079637731         0.15503451       6.223935e-02       0.0203861980        -0.31159126         0.10664368         0.22892309        0.049192090         0.18292270         0.10162373         0.19409459       -0.004813772        -0.08510377       -0.099590371      -0.1592289695        -0.14987100        0.008425516       -0.293152578        -0.28643062       -0.040028563         0.18403042        0.088763148        -0.17183112        -0.07892018       -0.072561676      -5.959037e-03        -0.33781668        0.018589804        0.192669206
> 

GSVA.Rcheck/tests/test_ssgsea_newapi.Rout


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> 
> ## 2023-11-10  axel: simple test script for method ssGSEA, new API
> 
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db


> library(GSVA)
> 
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
> 
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
> 
> p <- 10000 ## number of genes
> n <- 30    ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+             dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
           s1         s2          s3         s4          s5
g1  1.4171739 -1.3444519 -0.99052898  0.4203395  1.30716224
g2 -0.7281951  0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754  0.09779699 -0.6792548 -0.09124045
g4  1.0735382  1.3156255  0.15588330 -1.8079608  0.48531108
g5  0.7229884 -0.9162342  1.93982245  0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+                    paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> ssgseaPar <- ssgseaParam(X, gs)
> ssgsea.es <- gsva(ssgseaPar, verbose=FALSE)
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
> dim(ssgsea.es)
[1] 100  30
> ssgsea.es[seq.int(min(nRowsToPrint, nrow(ssgsea.es))),]
               s1           s2          s3           s4           s5           s6          s7          s8           s9          s10           s11          s12          s13          s14         s15          s16          s17          s18         s19          s20         s21          s22         s23         s24         s25         s26          s27         s28          s29          s30
gs1   0.050046308  0.153445680  0.06440230  0.245928762 -0.039281351 -0.009166497  0.15513670  0.05825828  0.075703720 0.2211977472  0.1909755963  0.213798011 -0.061198758  0.067211285  0.14116126  0.172193009 -0.076107078  0.146208482  0.27199640  0.027375283  0.25958081 -0.106935451  0.01955332  0.31199267  0.18689996 -0.02538041  0.025160949  0.10202723  0.317960731 -0.077195317
gs2   0.081171485  0.161930448  0.19635614  0.226977722  0.084705475  0.122712065  0.25375216  0.06124718  0.245645786 0.0213152908  0.1553307677  0.123198146  0.188559702  0.090605381  0.13634300  0.045583205  0.117061823  0.170602582  0.25518183  0.162276466  0.09782367  0.004672292  0.14429067  0.23905295  0.15842119  0.17958482  0.278174676  0.12969068  0.012534148  0.036195649
gs3   0.155539308  0.008842632  0.17903935  0.114060106  0.107208758  0.184963019  0.11327060  0.17081118 -0.110611530 0.3187327429  0.0896885519  0.169232189  0.292515661 -0.109522283  0.39211201  0.036070929  0.141878189  0.192157970 -0.01831034 -0.028374783 -0.31739185  0.238016028 -0.06330888  0.16972085  0.38536400  0.19915210  0.020583043  0.25012966  0.186034734  0.232849532
gs4   0.100407452  0.178458402  0.10660518  0.159340098  0.150690547  0.242066049  0.09044728  0.13980211  0.072737831 0.1082857648  0.0915659224  0.136234969  0.061324248  0.115973559  0.28107234  0.138134111  0.214028524  0.086667572  0.09385724 -0.029785545  0.12586634  0.082632971  0.17808866  0.21133946  0.16632346  0.17155219  0.102324377  0.20705832  0.099089588  0.290472119
gs5   0.194033575  0.062793781  0.04848598  0.217341759  0.191914352  0.129512577  0.15090606  0.27146643  0.219627621 0.1165628347  0.1379487730  0.152302042  0.099901051  0.205679023  0.12986947 -0.004963142  0.190709801  0.174401755  0.04427775  0.082055507  0.10896263  0.068825475  0.07614058  0.13558182  0.10568477  0.11492927  0.188047631  0.14065184  0.172431746  0.144376505
gs6   0.025988630  0.233512601  0.04485374  0.149671413  0.164451696  0.223396448  0.13735451  0.15303178  0.125071887 0.2456561342  0.1220311380  0.059904884  0.034633361  0.006225782  0.14294390  0.105914640  0.118989560  0.234603796  0.05542837  0.175273940  0.12454592  0.055488242  0.25878309  0.07422275  0.08197481  0.27581388  0.111785007  0.10024739  0.028180564  0.147366318
gs7   0.121579155  0.248146053  0.20935405  0.098421904  0.005775149  0.141790217 -0.04190763  0.02191384  0.225359966 0.0003605319  0.1938341367  0.218166804  0.234711429  0.171511561  0.14870761  0.004943158  0.168428297  0.131664402  0.16148235  0.046908832  0.09016756  0.199893820  0.17366414  0.10055547  0.08930753  0.16771471  0.141067369  0.20184683  0.113755713  0.062537548
gs8   0.175951236  0.104036859  0.16715411  0.066581368  0.124736570  0.107121162  0.15227018  0.13551209  0.066044097 0.0704654595  0.2006164228  0.164797947  0.149994634  0.063391557  0.20349135  0.205315802  0.006936426  0.130049520  0.17910706  0.061817683  0.05195776  0.059676074  0.18475605  0.10873217  0.25833265 -0.05691274  0.152978263  0.16063583  0.115089785  0.086840652
gs9   0.012967426  0.095461238  0.31825984  0.426422393 -0.206013607 -0.324946275  0.08738730 -0.14420537  0.061606991 0.1058375433  0.3407494698  0.060782012  0.036354426  0.158643593  0.02660000  0.070018029  0.295526014  0.370485869  0.31177819 -0.048490861  0.14293901 -0.052155641  0.39443397  0.18784912 -0.02491664  0.42956908  0.004366843 -0.09351215  0.539660825  0.194470958
gs10  0.310450557 -0.155381634 -0.04662343  0.069903089  0.235460838  0.136094565  0.35534293  0.14451145  0.032811542 0.2783927322 -0.0003708892  0.364801135  0.085153930 -0.007025257  0.31541487  0.214116068  0.076379415  0.300464786  0.02436326  0.014174550  0.29010030  0.353773500 -0.14036272  0.31414362  0.07517937 -0.36240056  0.135363804 -0.03291463  0.153638245 -0.006111044
gs11  0.148113831  0.288039198 -0.01173447 -0.125211500  0.422877496  0.368992470  0.31511056  0.11703945  0.119067901 0.2969431165  0.1767112563  0.269003140 -0.126699232  0.063371585 -0.15584600 -0.181509478 -0.252102260  0.084592131  0.41484382  0.102741674  0.19038088  0.155665264  0.11205065  0.18151841  0.07962262 -0.12707952 -0.043348625  0.52382483  0.471772841  0.192133037
gs12  0.191362265  0.075821020  0.10101534  0.015589766  0.118539915  0.150230064  0.11740963  0.09874133  0.196307720 0.1336100372  0.2243542624 -0.037860476  0.035827902  0.019570602  0.05739397 -0.086404343  0.090407547  0.090844017  0.11188849  0.250652019  0.15642076  0.100960304  0.13217523  0.09147595  0.14935140  0.07679723  0.164747489  0.10884565  0.021875796  0.224835781
gs13  0.291858703  0.346475308  0.21825672  0.130219327 -0.045991328  0.234867271  0.34027295  0.11127727  0.246617815 0.3200429439  0.0493766799  0.008390396  0.100929397 -0.036222987  0.09552925  0.116070504  0.050409473  0.117373720  0.33645267  0.196460577  0.28151964  0.250645402  0.00786962  0.16471272  0.26987750  0.14003078  0.274510723 -0.06972362  0.111250445  0.031727494
gs14  0.190335262 -0.064441167 -0.14720764  0.313073121  0.184851969  0.034311372  0.29316721 -0.12497882  0.099774835 0.0064937265  0.1376061089  0.105283947  0.322046351  0.260972829  0.22468693  0.113901307  0.002316888  0.174550489  0.03848764  0.149291379  0.16606614  0.171358521 -0.23264680  0.06333781  0.26046384  0.14647155  0.061583955  0.07893101  0.084042439  0.241795872
gs15  0.217913642  0.141978343  0.21703088  0.061088530  0.048906153  0.109096881  0.04362714  0.21225573  0.180978230 0.1203085545  0.0888328589  0.183656898  0.074251458  0.108846516  0.01790968  0.222984303  0.115016738  0.124120115  0.11555410  0.162960343  0.12134445  0.108547160  0.18775900  0.20267430  0.21813681  0.05956895  0.081086983  0.04401661  0.004584748  0.113053205
gs16  0.008372193  0.198823477  0.02924146  0.187858615  0.054689339  0.068398317  0.10730408  0.05120743  0.070935563 0.0784796201  0.0060339391  0.097386464  0.181367848  0.060028026  0.18405253  0.129145564  0.127244708  0.083034338  0.06835057  0.111075315  0.12519485  0.101386193  0.10027865  0.07630206  0.11786623  0.12151097  0.076099407  0.06340149  0.199302468  0.107472386
gs17 -0.021209113  0.041234441  0.15849782  0.140830687  0.094989136  0.050310553  0.27875609  0.19671686  0.224090634 0.0823059119  0.1446622842  0.073610528  0.181135843  0.128995630  0.18515033  0.043619934  0.156832276  0.139817243  0.12097998  0.094078972 -0.01250999  0.263313353  0.18157262  0.06476920 -0.02611791  0.19436554  0.098776218  0.15857389  0.086521226  0.140174046
gs18  0.224221766  0.208703330  0.19566999  0.277362679  0.086022967  0.155782407  0.21984017  0.06224476  0.184311430 0.0746810884  0.1500112520  0.031591001  0.218220154  0.085782290  0.05403013  0.239733411  0.225608272  0.080410483  0.12419147  0.087988742  0.09109210  0.118154979  0.18042347  0.15034333  0.05419059  0.06131728  0.135992696  0.05116987  0.008007108  0.258350779
gs19  0.060496086  0.192359984  0.06580294  0.039342129  0.056421351 -0.050071255  0.09835605  0.19838255  0.232365057 0.1878213634  0.0597175977  0.113955441  0.138654652  0.118112400  0.02948580  0.183873151  0.295382463  0.084940527  0.01555718  0.237711415  0.15405004  0.113893226  0.01261294  0.08150703  0.13679835  0.17664342  0.264724147  0.09871800  0.219093664  0.229287431
gs20 -0.002331868  0.104835345  0.19095558  0.196525176  0.230511428  0.196485997  0.20691704  0.06292261  0.195484717 0.0748935120  0.2274655731  0.234958644  0.100720547  0.098787011  0.01322616  0.215826190  0.107383744  0.272734953  0.14006653  0.128606660  0.17526232  0.154071267  0.20185690  0.16029505  0.11767405  0.04019989  0.087560954  0.12297014  0.120555888  0.165784444
gs21  0.235531812  0.174101071  0.04331386  0.066700909  0.161550174  0.127508845  0.22978825  0.07748909  0.142407170 0.1262273951  0.0698341132  0.023900707  0.157264078  0.064306708  0.19037040  0.022272735  0.085059711 -0.030333898  0.10370986  0.041024634  0.15543738  0.156630569  0.11755610  0.14827641  0.09418257  0.26082349  0.175064303  0.10818015  0.134571164  0.137789233
gs22 -0.047650929  0.186841315  0.03222656  0.119471610  0.193877261 -0.031790084  0.29277495  0.07689763 -0.019411157 0.0595495594  0.3807452330  0.071668171  0.135528037  0.177342300  0.18766862  0.143986114  0.138391599  0.137573467  0.11420368  0.222882426  0.06096151  0.160136193  0.37542340  0.34681913  0.02224170  0.20670334  0.053159207  0.38290841  0.093613064  0.168206100
gs23  0.144199311  0.186850465  0.09563174  0.191503633  0.197926948  0.183687676  0.08857992  0.08438396 -0.002354026 0.1015861893  0.1556606664  0.149031544 -0.003876439  0.220881227  0.19108193  0.128779302  0.115583034  0.128810013  0.21233978 -0.001768056  0.13275623  0.154387029 -0.06742232  0.07991395  0.15197278  0.23716849  0.161038324  0.06541124  0.045781546  0.096529440
gs24  0.244519906  0.255495479 -0.02212643  0.007561398  0.045577309 -0.009892961 -0.04971968  0.19698687 -0.078933887 0.0414502136  0.3742714753 -0.050544352  0.013590683  0.003608241 -0.34825490  0.415098155  0.138025957 -0.001864139 -0.37016901  0.117420895  0.37252626 -0.116751635  0.32072205 -0.06702968  0.11533867  0.21077948 -0.041474525  0.03217032 -0.044872621  0.165434542
gs25  0.193601681  0.091245208  0.18463093  0.100724310  0.055381436  0.002669872  0.08514397  0.05620041  0.124029775 0.1800670374  0.1742834586  0.170840558 -0.034319609  0.177918537  0.09381717  0.145284931  0.208953543  0.324830001  0.16350519  0.037554150  0.26681356  0.012083285  0.28774452  0.13816374  0.05451236  0.10453580  0.280375699  0.12512785  0.135834785 -0.038267879
> 
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+                     featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+                     sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+                                       grep("^REACTOME", names(c2BroadSets)),
+                                       grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- ssgseaParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+                       minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
                                                    NA19099      NA18523     NA19144     NA19137      NA18861     NA19116     NA19130       NA19131      NA19119     NA19152     NA19153      NA19140     NA19138     NA18522     NA19192     NA19193     NA19239       NA19238      NA19210     NA19201     NA19172      NA18870     NA18858     NA18852      NA19159      NA18855     NA19204      NA18501      NA19127      NA19098      NA19093      NA18856     NA18912     NA18517     NA18502      NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                  0.21698978  0.190101718  0.20525435  0.21623854  0.228779757  0.20936853  0.22506971  0.2234235687  0.220780261  0.21444921  0.21903592  0.220664804  0.20924941  0.21012248  0.20502111  0.19985724  0.19721755  0.1913957094  0.225134348  0.21709921  0.20425590  0.201712948  0.19379346  0.23122161  0.221525326  0.212463371  0.22792181  0.221128254  0.204351144  0.218947974  0.222579602  0.229420498  0.22060750  0.20299621  0.21904369  0.215493102
KEGG_CITRATE_CYCLE_TCA_CYCLE                     0.32433043  0.330666662  0.31869186  0.30766734  0.322670342  0.31519248  0.31986814  0.3185006606  0.329706974  0.31265435  0.32676917  0.331734849  0.31520463  0.32288700  0.31043279  0.31220717  0.30722070  0.3168181879  0.320522995  0.32920820  0.31023554  0.313528956  0.32324416  0.32442285  0.307746225  0.302000352  0.31422539  0.325061712  0.324433443  0.320805701  0.313120479  0.322340322  0.32303440  0.31470507  0.32982874  0.322774682
KEGG_PENTOSE_PHOSPHATE_PATHWAY                   0.32613456  0.292246085  0.32171779  0.31922331  0.327342371  0.32285413  0.31703691  0.3267972444  0.317799481  0.30548746  0.32071494  0.325200548  0.31574521  0.32222525  0.30445849  0.31198274  0.30056356  0.3175363433  0.313248908  0.31537383  0.31498239  0.312138133  0.31157241  0.31348063  0.313260085  0.305543436  0.31306655  0.318602720  0.309415331  0.316959102  0.307805386  0.319474001  0.30318847  0.31470071  0.31941053  0.326759498
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS    0.14142675  0.152207936  0.14238572  0.07942752  0.105050011  0.12961280  0.11296245  0.1601888948  0.141345242  0.09869492  0.16412075  0.158434716  0.10823031  0.17672793  0.13428568  0.11392145  0.14170168  0.1428868433  0.146955737  0.14818936  0.17164951  0.138839694  0.12229281  0.11673825  0.109550600  0.069456602  0.14040696  0.182050959  0.114699787  0.189319064  0.130300608  0.111638487  0.14391952  0.12318954  0.12224946  0.137976483
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM             0.15550203  0.118146628  0.14707933  0.18705703  0.199943713  0.16410186  0.16813615  0.1802125060  0.170259262  0.18671240  0.18252531  0.164279928  0.16794179  0.17149276  0.16625970  0.14528892  0.13398404  0.1378452121  0.169092878  0.19220147  0.19047757  0.157694632  0.12722729  0.18630354  0.195343439  0.176599720  0.19802720  0.161573744  0.152184181  0.173797461  0.187295272  0.197591583  0.17232864  0.16136207  0.17911558  0.180031024
KEGG_GALACTOSE_METABOLISM                        0.11149473  0.103217880  0.11085844  0.13741766  0.165952026  0.14418332  0.12726683  0.1370210459  0.142805283  0.15242781  0.15221252  0.149682255  0.15018345  0.14626213  0.11999955  0.11557928  0.11593006  0.1148701557  0.149672283  0.16891575  0.16494312  0.123919369  0.09211866  0.14937665  0.176575543  0.129061875  0.17075453  0.137859374  0.112830567  0.139888692  0.144650768  0.159081145  0.13428014  0.12448791  0.15631215  0.169827420
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM           0.04198555 -0.032292278  0.01406413 -0.01064716 -0.022308338 -0.03194340 -0.01037135  0.0661161558 -0.007360627 -0.02923521  0.01141517  0.001497673 -0.01420985  0.03438381 -0.03203514 -0.01804054 -0.01538922 -0.0026678425  0.027398691 -0.04882214 -0.11561188 -0.008509357 -0.01203473 -0.02089645  0.001083068 -0.003061739 -0.11355468  0.027193644 -0.020507654  0.050375480  0.023851383  0.004333629  0.02757450 -0.01461678 -0.01931510  0.006947649
KEGG_FATTY_ACID_METABOLISM                       0.19144010  0.177618186  0.19229237  0.18162156  0.195013260  0.17285053  0.18737923  0.2094263692  0.189298006  0.17744684  0.17726086  0.187594417  0.17484769  0.18064373  0.17580318  0.16279037  0.17715535  0.1847771315  0.187298535  0.17615351  0.15131681  0.184344838  0.17544154  0.18540490  0.164558082  0.179209973  0.15666232  0.189591897  0.183358359  0.189661362  0.185937924  0.195641028  0.20399213  0.18301653  0.17977089  0.185912168
KEGG_STEROID_BIOSYNTHESIS                        0.29508326  0.295486909  0.26286536  0.27906495  0.291220515  0.28574075  0.30491564  0.3028446031  0.306065643  0.26781522  0.29464863  0.281727962  0.28372727  0.30309918  0.30917324  0.26593252  0.26945212  0.3018824439  0.272449306  0.28920242  0.27852421  0.273019343  0.28299044  0.28594314  0.297497744  0.264419747  0.26785147  0.276188961  0.286487520  0.308034927  0.289095316  0.299848680  0.29269188  0.29943769  0.29468427  0.287313424
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS             -0.03581753 -0.092130799 -0.04761225  0.05891582 -0.123502963 -0.08482548 -0.02276997 -0.0448787260 -0.064166255 -0.15073085 -0.07715570 -0.027840150 -0.03137614 -0.08997226 -0.12858747 -0.15452411 -0.15192399 -0.0008490506 -0.141927194 -0.12439918 -0.14957231 -0.052218742 -0.06096819 -0.03648457 -0.146524551 -0.129025468 -0.15339387  0.017340701  0.013213935  0.021006051 -0.008592746 -0.079442545 -0.01531376 -0.09542512 -0.12181560 -0.100962579
KEGG_STEROID_HORMONE_BIOSYNTHESIS               -0.00603142 -0.048459074 -0.07974466 -0.01648330 -0.091376743 -0.04645294 -0.05783215 -0.0077100648 -0.032440674 -0.04925962  0.01257962 -0.027085733 -0.05133063 -0.03464357 -0.09107591 -0.04604528 -0.06313163 -0.0037229305 -0.083744196 -0.04403506 -0.07403528 -0.041751578 -0.06718897 -0.06224135 -0.022813686 -0.063619976 -0.05046193 -0.046775240 -0.007732293 -0.031014587  0.038972593 -0.058183774  0.01398730 -0.04158946 -0.10044713 -0.022828144
KEGG_OXIDATIVE_PHOSPHORYLATION                   0.23470278  0.265724094  0.26337583  0.24721506  0.255184437  0.25137871  0.25453660  0.2566994039  0.246493165  0.25745496  0.25786805  0.247495875  0.25321032  0.26043249  0.24844391  0.24615206  0.25180784  0.2621473829  0.253121007  0.24466091  0.24444401  0.248324354  0.24596943  0.26085564  0.252493166  0.259461341  0.25704694  0.244689333  0.244937049  0.247126050  0.249275632  0.253150955  0.25606696  0.26126201  0.26134069  0.248688913
KEGG_PURINE_METABOLISM                           0.11282696  0.113448858  0.13052367  0.12872555  0.130498773  0.12514834  0.12708974  0.1254518508  0.114374092  0.11746139  0.12720504  0.123909976  0.12501986  0.12926543  0.11864833  0.11039303  0.11837407  0.1306561048  0.120874877  0.11874917  0.12461513  0.118754355  0.11004336  0.12341313  0.111728921  0.125220817  0.12599093  0.120422095  0.116669899  0.120942649  0.125716426  0.120651681  0.12066825  0.12286847  0.11781015  0.119089666
KEGG_PYRIMIDINE_METABOLISM                       0.17757771  0.175394817  0.19858724  0.19679890  0.184451412  0.18857531  0.19443581  0.1913521689  0.176616057  0.18757690  0.18742386  0.190866974  0.17707165  0.19343157  0.18609589  0.18058113  0.18517942  0.1962563816  0.174386960  0.18912297  0.18783617  0.175188077  0.17750981  0.19040712  0.177216013  0.198853296  0.18467609  0.173153515  0.179616517  0.173598395  0.177726615  0.185542608  0.19263573  0.19211082  0.17683259  0.184513099
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM  0.10989042  0.093058240  0.09075182  0.09975330  0.110553924  0.08932985  0.10833717  0.1022932484  0.098714538  0.09452201  0.10412503  0.112821342  0.09845573  0.09864529  0.10839464  0.10195788  0.09460140  0.0890330658  0.114926416  0.12373452  0.09891343  0.096051085  0.08806549  0.11101748  0.101678482  0.090367626  0.10014984  0.113927079  0.088757290  0.111944663  0.101911619  0.091610295  0.08631087  0.10449490  0.09680798  0.113666733
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM     0.07589995  0.013164475  0.03073650  0.05497730  0.075187517  0.04629436  0.05684194  0.0721291176  0.091914474  0.05519977  0.08746496  0.050067541  0.05965801  0.06067566  0.08409397  0.10238484  0.01501362  0.0045650662  0.049144983  0.07054669  0.05116744  0.045186268  0.05137738  0.06424885  0.085465393  0.053004029  0.06129235  0.050492310  0.064513199  0.069147728  0.067789023  0.075006091  0.03311465  0.05179666  0.09353812  0.069833588
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM          0.25896290  0.229197097  0.23915083  0.24454874  0.251021905  0.23616587  0.24671301  0.2542987322  0.256828445  0.24146968  0.26145521  0.245522688  0.24379502  0.24900959  0.26862910  0.25530625  0.22947514  0.2349385424  0.237967026  0.24111547  0.26557949  0.234639477  0.23412745  0.23301781  0.258395796  0.215746987  0.23465476  0.256687996  0.239987950  0.250370070  0.237026241  0.252743721  0.22651684  0.23865720  0.25741554  0.244270299
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION   0.18843747  0.186649426  0.17530857  0.15633381  0.178282757  0.18033157  0.18581500  0.1963894497  0.191659866  0.14190172  0.20151595  0.181514394  0.18800238  0.18208434  0.18884446  0.17012565  0.16953990  0.1676338847  0.183699227  0.19745711  0.16337494  0.161194552  0.15788716  0.18351104  0.171161284  0.163754665  0.15047991  0.196948812  0.185610694  0.198192986  0.174172878  0.182779264  0.17802037  0.16062757  0.19890618  0.189941640
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS  0.28568183  0.282786776  0.24961716  0.24491634  0.270528716  0.29605800  0.25836996  0.2521218808  0.281679472  0.24721670  0.32053768  0.274690843  0.28302481  0.30038542  0.30322093  0.29120270  0.28253548  0.2579537498  0.267208046  0.32453395  0.29189041  0.267396603  0.24747811  0.28281020  0.293967599  0.262178623  0.29429367  0.269346291  0.263428379  0.266865452  0.261098171  0.251262879  0.25119395  0.28412517  0.31296991  0.299112229
KEGG_LYSINE_DEGRADATION                          0.11363066  0.093971946  0.11756645  0.11921555  0.114150109  0.11417055  0.11382771  0.1282543770  0.110373515  0.10264637  0.10896281  0.119922709  0.11111424  0.09923486  0.10398550  0.09158226  0.11014421  0.0992105519  0.114396655  0.11105307  0.10519398  0.095412052  0.09666140  0.10310679  0.108674463  0.114399506  0.09091906  0.108210445  0.111356587  0.117142092  0.103818204  0.110313192  0.10414576  0.09228489  0.10733176  0.111914878
KEGG_ARGININE_AND_PROLINE_METABOLISM             0.12738384  0.120646580  0.12800721  0.12780121  0.140190182  0.11234716  0.13886310  0.1363147983  0.118339180  0.12495239  0.13387648  0.119717717  0.12674429  0.11413969  0.12760775  0.12051016  0.11112441  0.1060723468  0.135207120  0.11384185  0.11270554  0.120444480  0.10890719  0.13671193  0.148306216  0.127590175  0.12033740  0.129990177  0.120085884  0.143513369  0.139267799  0.139711646  0.12631236  0.12302536  0.13671696  0.129915338
KEGG_HISTIDINE_METABOLISM                        0.01037506 -0.009232361 -0.02503732 -0.04007054 -0.004116879 -0.02891744 -0.02515002  0.0005514458 -0.015393247 -0.03216059 -0.03701174 -0.018066447 -0.04417577 -0.03579879 -0.02417860 -0.02971581 -0.02648223 -0.0314952886  0.009196744 -0.04701498 -0.06879069 -0.022838496 -0.03099772 -0.03704899 -0.025519728 -0.039940345 -0.08649494  0.003895911 -0.029842438 -0.000484478 -0.020239498 -0.027308388 -0.01132841 -0.03055363 -0.02153193 -0.036015417
KEGG_TYROSINE_METABOLISM                         0.06714488  0.053002829  0.05753161  0.04337986  0.057065867  0.05794194  0.05847814  0.0507298323  0.058615853  0.04701795  0.05759954  0.046542561  0.04954693  0.06556692  0.07181820  0.05370509  0.05763770  0.0690302934  0.044285470  0.04352433  0.06313789  0.067191326  0.04882973  0.05342728  0.052557681  0.041207045  0.04378767  0.064256091  0.055186897  0.048349590  0.069931678  0.042623088  0.06573735  0.06531103  0.05853359  0.057231880
KEGG_PHENYLALANINE_METABOLISM                    0.11960304  0.096377593  0.09464200  0.09061793  0.091267769  0.09170094  0.09990226  0.0976280231  0.105007097  0.08739764  0.09597757  0.092011591  0.10469452  0.09925149  0.10437604  0.10710066  0.07942615  0.0989797292  0.119065427  0.09925727  0.10453704  0.086330586  0.09687302  0.10521245  0.097635425  0.085996013  0.09971671  0.107245185  0.084152959  0.091621331  0.102207053  0.107399793  0.10262963  0.09509872  0.08816275  0.098383108
KEGG_TRYPTOPHAN_METABOLISM                       0.12707074  0.135904404  0.12002196  0.10198472  0.105456181  0.10258554  0.11263398  0.1471089408  0.134184467  0.09404104  0.12387419  0.114507791  0.10212085  0.12955711  0.09526545  0.11899775  0.10760770  0.1237862285  0.125934177  0.11873044  0.06658891  0.112588368  0.11212948  0.10011186  0.118024833  0.113614802  0.09153418  0.132524487  0.110393708  0.120368868  0.125229509  0.116181945  0.14682099  0.11978502  0.10429972  0.118580441
> pickrellPar <- ssgseaParam(pickrellCountsArgonneCQNcommon_eset,
+                          canonicalC2BroadSets, minSize=5, maxSize=500)
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
> exprs(esrnaseq[seq.int(min(nRowsToPrint, nrow(esrnaseq))),])
                                                     NA19099      NA18523     NA19144     NA19137     NA18861     NA19116     NA19130     NA19131     NA19119     NA19152      NA19153     NA19140      NA19138     NA18522     NA19192      NA19193     NA19239      NA19238     NA19210     NA19201     NA19172     NA18870     NA18858      NA18852      NA19159      NA18855     NA19204     NA18501       NA19127     NA19098     NA19093     NA18856     NA18912     NA18517     NA18502     NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                  0.256075759  0.234440285  0.22365541  0.25164814  0.25617134  0.22440002  0.26825331  0.24363221  0.22303626  0.24453749  0.241659658  0.24784931  0.240912314  0.26440850  0.25175671  0.221994177  0.25951673  0.257749187  0.23737636  0.23373922  0.24102923  0.24394811  0.24421325  0.253552534  0.230189600  0.233117341  0.25308269  0.25087262  2.352772e-01  0.25308477  0.25405537  0.23991583  0.23478740  0.24563546  0.25646515  0.25071702
KEGG_CITRATE_CYCLE_TCA_CYCLE                     0.276806659  0.263840724  0.24698443  0.27529933  0.27555689  0.24975236  0.28827170  0.26740093  0.22453250  0.25824366  0.264578233  0.26626941  0.267999750  0.27293682  0.26955574  0.218915231  0.28141656  0.274122454  0.25380024  0.25929889  0.26072040  0.26865139  0.27076349  0.265378539  0.244259988  0.241425821  0.28531051  0.28111746  2.409079e-01  0.26208495  0.26235839  0.27393384  0.25428617  0.26899433  0.27380231  0.26464529
KEGG_PENTOSE_PHOSPHATE_PATHWAY                   0.308157944  0.298087515  0.29014344  0.31316947  0.31075726  0.29580575  0.33150923  0.30911766  0.27215128  0.29310006  0.318390367  0.31750877  0.303315781  0.32990830  0.31603865  0.276156993  0.32137928  0.328904420  0.28873356  0.28984710  0.29765756  0.29417757  0.30408635  0.309010795  0.284366223  0.286933996  0.32289659  0.31674788  2.939716e-01  0.30287805  0.30290168  0.30124596  0.29981504  0.30880460  0.29585316  0.31112043
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS    0.072900627  0.058114116  0.05095095  0.05552091  0.06878391  0.07768438  0.08213775  0.09250688  0.03556826  0.09156620  0.097878249  0.06956272  0.081520495  0.14591883  0.10114649  0.031874974  0.09204189  0.115726730  0.08879480  0.08133511  0.11303741  0.04597980  0.05930134  0.091652196  0.045442518  0.015179733  0.11243384  0.13618849  5.819542e-02  0.07901269  0.10767281  0.06217197  0.10083457  0.07884946  0.04823275  0.08069438
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM             0.179143833  0.181466412  0.18164218  0.20648051  0.16508263  0.15692126  0.20526979  0.18220460  0.12828973  0.18948921  0.194624757  0.18678502  0.191651374  0.18621396  0.21686165  0.163982758  0.20153270  0.213681011  0.17124101  0.18326784  0.17747109  0.18055651  0.18666452  0.208603904  0.182698854  0.186529878  0.20249678  0.14324407  1.692164e-01  0.17589451  0.20061610  0.16286430  0.16195031  0.19908025  0.18482874  0.20501174
KEGG_GALACTOSE_METABOLISM                        0.181131627  0.159926813  0.16270579  0.20573093  0.18044266  0.15543518  0.21952142  0.17843456  0.12359001  0.18349838  0.199111340  0.19452033  0.190574177  0.19551040  0.22253670  0.149654098  0.20567552  0.200581366  0.17030505  0.18223148  0.18954484  0.17613758  0.17006314  0.194920826  0.198422033  0.192448054  0.22245521  0.15408689  1.635711e-01  0.17252060  0.20589447  0.15895753  0.15412635  0.18901486  0.18924635  0.20842567
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM           0.076244940  0.080303827  0.01896975  0.05351930  0.05634166  0.03667802  0.08143338  0.05261833  0.02095408  0.09594147  0.046490176  0.03601321  0.072687156  0.13959149  0.04107588  0.001557203  0.08580840  0.109000508  0.05530623  0.01833645 -0.08023056  0.01932496  0.06300957  0.066003820  0.023771292  0.007102489  0.03086936  0.10270298 -3.157042e-03  0.05314639  0.07495172  0.08280269  0.05626948  0.04257381  0.06298584  0.07433531
KEGG_FATTY_ACID_METABOLISM                       0.189817509  0.170872559  0.14155879  0.19190458  0.20061758  0.16220943  0.20719303  0.18088378  0.16687336  0.17684223  0.169286125  0.17914218  0.178915532  0.20998722  0.17201976  0.131109962  0.20936840  0.197325741  0.16514248  0.15827116  0.16387239  0.17860585  0.18319739  0.188238171  0.113651303  0.130750066  0.17770022  0.19465482  1.597647e-01  0.18876629  0.18911247  0.18967056  0.15979790  0.16688397  0.17911784  0.19754478
KEGG_STEROID_BIOSYNTHESIS                        0.224283008  0.183502868  0.10641865  0.15431521  0.20673953  0.19381572  0.19919988  0.19375955  0.13759180  0.13279097  0.166353748  0.15479731  0.201859944  0.18441257  0.20240525  0.138935955  0.16161930  0.187730965  0.12780607  0.17277089  0.17211107  0.17687687  0.20523660  0.178291553  0.222139792  0.187421826  0.17910855  0.15862534  1.563029e-01  0.17970860  0.21186843  0.18641454  0.20553433  0.21995063  0.24238713  0.17376305
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS              0.007298097 -0.045231480 -0.05615631  0.07155428 -0.03778360 -0.06475813 -0.01631200 -0.01120530 -0.07059793 -0.07173726 -0.040573532 -0.01433368  0.005000649  0.05037597 -0.04733764 -0.070668142 -0.04251391 -0.016724966 -0.03493901 -0.06316513 -0.04576571 -0.03089320 -0.02209954 -0.003440324 -0.082490284 -0.065017438 -0.04750185 -0.03693552 -2.405233e-05  0.03741013  0.04625340 -0.02630856 -0.04838299 -0.05724028 -0.04066866 -0.03635462
KEGG_STEROID_HORMONE_BIOSYNTHESIS               -0.046018108 -0.093294319 -0.13746745 -0.05837140 -0.11437771 -0.04362896 -0.07770349 -0.07282807 -0.09993655 -0.05986338 -0.051748220 -0.07057083 -0.081288974 -0.04819890 -0.08749854 -0.080358972 -0.09355664 -0.072350610 -0.13131875 -0.06410751 -0.13561358 -0.09017416 -0.11589119 -0.085631744 -0.094304978 -0.119555451 -0.07166260 -0.03448379 -6.616326e-02 -0.10521967  0.02700273 -0.04856765 -0.05304776 -0.11560595 -0.12890981 -0.06549103
KEGG_OXIDATIVE_PHOSPHORYLATION                   0.290044085  0.306375054  0.26041452  0.29564165  0.29454677  0.28682961  0.31516942  0.29225539  0.29624881  0.28190329  0.288965873  0.29838803  0.296122751  0.30714929  0.29408922  0.298005863  0.29592505  0.304180875  0.28081795  0.28727692  0.29838136  0.30109527  0.29148313  0.294331078  0.252378384  0.264546548  0.29654867  0.30641064  3.067693e-01  0.28941630  0.30210492  0.30197862  0.31189519  0.28625608  0.28901836  0.28725201
KEGG_PURINE_METABOLISM                           0.121552424  0.114160233  0.11048165  0.13105255  0.11833540  0.10870679  0.12953106  0.12047921  0.08446782  0.11231713  0.112887563  0.11536146  0.105467789  0.13155054  0.12002126  0.113011238  0.12896358  0.123095976  0.11982023  0.10583172  0.10912082  0.11113234  0.10512995  0.109356079  0.099193918  0.103015548  0.12720303  0.13748276  1.143107e-01  0.12051435  0.10972889  0.11378580  0.10276405  0.11768950  0.10730690  0.11186763
KEGG_PYRIMIDINE_METABOLISM                       0.159729043  0.145500125  0.14730788  0.17410916  0.15340765  0.14791645  0.16855838  0.15892991  0.11381615  0.15157687  0.147076658  0.15194721  0.127133366  0.17182833  0.15867282  0.142850963  0.16307797  0.161493787  0.14783129  0.14154301  0.14666943  0.14191003  0.14540419  0.146472588  0.114588161  0.131180250  0.16581516  0.18090777  1.515887e-01  0.16056284  0.13622778  0.16268189  0.13979801  0.15559869  0.13630535  0.15387683
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM  0.112712342  0.074567957  0.08695191  0.09240285  0.11298142  0.09506027  0.09739823  0.07764648  0.10950728  0.07593407  0.076879433  0.07931452  0.081605261  0.10786533  0.09769440  0.046974792  0.08948356  0.076841077  0.09165978  0.07828511  0.07203344  0.08737763  0.06590033  0.087495399  0.073193496  0.070563832  0.10778181  0.09237847  6.349400e-02  0.12215027  0.08568016  0.06775927  0.05945302  0.08035606  0.08620309  0.09688249
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM     0.063414089  0.008780948  0.05935336  0.06694159  0.06788012  0.04426421  0.03357666  0.04745672  0.07210759  0.05011682  0.019676287  0.05273708  0.007465601  0.07973086  0.04674425  0.006592034  0.03645575  0.007696429  0.06004590  0.01417259 -0.02089575  0.04782863  0.03721318  0.033513757  0.059026917  0.026399449  0.05354070 -0.01859829  3.487693e-02  0.09841955  0.03620653  0.02255710 -0.01427914  0.03857687  0.09608318  0.07059776
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM          0.234037901  0.189794344  0.20539118  0.22853483  0.22730123  0.19920525  0.19855436  0.22105176  0.21859510  0.21569681  0.192366034  0.19664087  0.202877108  0.24438081  0.22600833  0.162641803  0.19791966  0.190679930  0.19704281  0.18167020  0.20854176  0.21380744  0.20125670  0.201679421  0.212128486  0.203347274  0.19742841  0.19425738  1.833991e-01  0.22861206  0.18710448  0.20444733  0.17838357  0.19817716  0.21897475  0.22036231
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION   0.149779799  0.130868968  0.11141194  0.15213162  0.15707673  0.12253970  0.17713191  0.13281221  0.14628124  0.12815576  0.154689122  0.13889347  0.148455429  0.18582753  0.14490882  0.100438410  0.16119649  0.158609790  0.12845278  0.13377880  0.12834048  0.13474814  0.13427088  0.163849429  0.097733032  0.107920307  0.15085656  0.15995811  1.171796e-01  0.15812798  0.14524879  0.14585176  0.13929386  0.12933917  0.15265580  0.15760441
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS  0.295088488  0.261790244  0.20437749  0.28756505  0.29611186  0.27215510  0.27635622  0.24614956  0.27920993  0.21961975  0.291130821  0.26258549  0.257402155  0.29814324  0.28934456  0.233740001  0.27822280  0.256193143  0.24326695  0.27454545  0.27722539  0.24789039  0.23212598  0.282819863  0.269379426  0.251031182  0.30807137  0.28499798  2.550574e-01  0.27349722  0.26662427  0.24049639  0.27670544  0.24397409  0.28271525  0.28462182
KEGG_LYSINE_DEGRADATION                          0.141718140  0.125418015  0.13297959  0.14283107  0.13473057  0.12203529  0.14719941  0.13385750  0.09491781  0.12236495  0.122241586  0.12711931  0.124884910  0.13829366  0.13755243  0.119698191  0.14226579  0.133886134  0.14436915  0.11175177  0.10560139  0.13083694  0.13813000  0.135265809  0.112781050  0.123216658  0.12973261  0.13564156  1.232322e-01  0.13580749  0.12462139  0.13626539  0.10525941  0.13533806  0.13567788  0.14158147
KEGG_ARGININE_AND_PROLINE_METABOLISM             0.135734485  0.123178563  0.10586472  0.12564409  0.14906498  0.11818042  0.14021365  0.12277557  0.09432899  0.11770248  0.140202156  0.10961800  0.124468602  0.13170402  0.12160081  0.090198152  0.12999175  0.127112384  0.11788380  0.11428458  0.11762968  0.13710845  0.11356352  0.130539368  0.104547379  0.117760260  0.12573673  0.11179118  1.059606e-01  0.14634309  0.13320560  0.10643279  0.10948257  0.12483287  0.14500055  0.12996698
KEGG_HISTIDINE_METABOLISM                       -0.030831971 -0.026347382 -0.05246956 -0.03817025 -0.03711451 -0.05239151 -0.02992710 -0.04339704 -0.04535416 -0.02246956 -0.068943683 -0.05028602 -0.063113563 -0.02707367 -0.05323869 -0.063275978 -0.03173868 -0.039525683 -0.02755053 -0.04591086 -0.06760272 -0.03666616 -0.02528646 -0.040320656 -0.044784334 -0.057674857 -0.06783511 -0.02118087 -4.757559e-02 -0.03079779 -0.03306480 -0.03762207 -0.04374289 -0.03096278 -0.01254511 -0.03899109
KEGG_TYROSINE_METABOLISM                         0.017578905  0.013796202  0.01327581  0.04762972  0.01224515  0.03037335  0.04467113  0.03453989  0.01369270  0.03704134  0.022735388  0.02729295  0.010396257  0.04953794  0.03065282  0.024393238  0.04694918  0.040233938  0.01044212  0.02743798  0.03891701  0.04757522  0.02613133  0.039036101 -0.011637129  0.007204219  0.04176325  0.02171444  5.394063e-02  0.02825620  0.04740187  0.02656193  0.05525311  0.01901562  0.06130051  0.03639278
KEGG_PHENYLALANINE_METABOLISM                    0.039387037  0.029253986  0.02751646  0.04138092  0.02542332  0.04090945  0.02613385  0.04694566  0.04409473  0.02669409  0.009505697  0.01810860  0.029763207  0.06543376  0.04989771  0.029176209  0.03209528  0.037862444  0.04544696  0.01254836  0.07318278  0.05544060  0.05343313  0.038427201  0.007101842  0.043387306  0.05281127  0.02894583  3.058806e-02  0.04347886  0.06369582  0.02896260  0.02467872  0.04490225  0.06313854  0.01977051
KEGG_TRYPTOPHAN_METABOLISM                       0.123296794  0.123012202  0.07613129  0.11525403  0.10856497  0.10334620  0.12704283  0.12708541  0.09159597  0.10202432  0.117859010  0.11469963  0.107325317  0.13152508  0.10459837  0.095553577  0.11230030  0.119066458  0.11008815  0.09174693  0.07821333  0.11181722  0.12158703  0.101828953  0.089254784  0.080564906  0.11224215  0.15882861  9.554444e-02  0.11310320  0.12619907  0.13651820  0.12255016  0.10789454  0.12458913  0.11276116
> 
> gbmPar <- ssgseaParam(gbm_eset, brainTxDbSets)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
                    TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up               -0.04270256          -0.1050256          0.12398917         -0.19785894          -0.0706204         -0.08331645         -0.04587976         -0.02691259           0.1493980          0.07636271           0.1292104         -0.02880156         -0.10622416          0.08485902         -0.02108542         -0.10255611         -0.04955077         -0.06055262          -0.1843912        -0.002264514        -0.000616764         -0.08413483          -0.1282847          0.10064219          0.16233229         -0.08391388         0.129510723         0.006051755          -0.0957773          0.05930173          0.07585551         0.122092770         -0.01523058         -0.17022164         -0.02753735         -0.09626334         -0.16239668          -0.1442122         -0.08378182         0.086702046         -0.06829592         -0.01859185         -0.10794134         -0.04824622         -0.02360036         -0.07829131          0.02113254          0.12831408         -0.05187672         0.021500630
astroglia_up                -0.24889633          -0.3181389         -0.16250310         -0.34518377          -0.2328486         -0.19025164         -0.20798167         -0.18978759           0.1634546         -0.18567656          -0.1220784         -0.14188750         -0.08219957         -0.18716765          0.08621605         -0.05093007         -0.23268801         -0.28527541          -0.2431186         0.280782610         0.051930564         -0.28603563          -0.2787882         -0.23358730          0.02706818         -0.17339069         0.007161405        -0.128829863          -0.2530055         -0.17991022          0.04954921         0.086976084         -0.19119326         -0.02761475         -0.10601965         -0.21094338         -0.17424458          -0.1764272         -0.25829321         0.183158653         -0.15279730         -0.15292932         -0.25484151          0.12260719         -0.09708606         -0.02624126         -0.03188327         -0.01503725         -0.17238517        -0.105109149
neuronal_up                  0.41365516           0.1370905          0.02258175          0.04140498           0.3739370          0.02504198         -0.09469289          0.21037816           0.2898127          0.02594733           0.4223345         -0.22630258         -0.21649319         -0.12661321          0.05458802         -0.15745561          0.22021627         -0.22540274          -0.1018101         0.108388420         0.248267146          0.15400529           0.2284369         -0.03153927         -0.06967695          0.04263526         0.379513854        -0.157687296          -0.1220727         -0.04305240          0.07266218        -0.007533977          0.14634095          0.25658376          0.45865011         -0.07414341          0.08676525           0.2972831          0.20881219         0.005408232          0.28084413         -0.11613621          0.17679797          0.32776928          0.01952200         -0.12391902         -0.24619662          0.49886083         -0.02607648        -0.001236969
oligodendrocytic_up          0.23276809           0.1579273          0.27834655          0.16541114           0.2967757          0.20073958          0.05308861          0.16548555           0.2960602         -0.06212319           0.2511061          0.23363850          0.49638543          0.20198656          0.02902960          0.30191162         -0.09088903          0.17653174           0.2923147         0.173427872         0.233041698          0.12377225           0.2739099          0.17169148          0.36533533          0.30762144         0.395886181         0.210670157           0.3295785          0.20726009          0.20552805         0.352208428          0.23866032          0.36220935          0.33072346          0.38151672          0.10382195           0.2867132          0.40519888         0.104315543          0.27453019          0.08890069          0.02961855          0.35470642          0.42481129          0.14658324          0.13577067          0.21517457          0.09820911         0.073203757
                    TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up               -0.12781345         -0.10424801        -0.003896955          0.23387421          0.25246844           0.3207035           0.1864102           0.2276360         0.264613462          0.16772316           0.1921236         0.150618790           0.2158142        1.480129e-01           0.2547912           0.2467531          0.16111355          0.19983249          0.07535168          0.28372256          0.14028380          0.14573966         -0.04131919          0.09047686           0.1447905          0.10384463         0.174769701          0.15962850          0.23867927         0.147562489          0.17203901          0.32877500          0.12467503           0.2831480          0.21697481           0.2582061         -0.04827454         0.070849773          0.10375364          0.05993822          0.14917783          0.03705593          0.28737667           0.1128391          0.15477895          0.16409778         0.143848674          0.08997557          0.25033466         0.200997387
astroglia_up                -0.33567021         -0.09558514        -0.267132320          0.27697125          0.04553025           0.1866003           0.1084145           0.1548024         0.115683387          0.08879166          -0.1794232         0.005649495          -0.1576545       -1.257789e-05           0.0727411           0.1555954         -0.05570396          0.07701213         -0.20774164         -0.04776384          0.13345907          0.02623989         -0.02663276         -0.05953059          -0.1011001          0.02571005         0.182406879          0.02375654          0.06349979         0.063565080         -0.03836509         -0.03293448         -0.03572666           0.1665919          0.16071904           0.2015802         -0.03462372         0.294133704          0.07912455         -0.09833367         -0.01426256          0.25177173          0.13323749           0.2085587          0.11625433          0.09270277         0.061118313         -0.01415236          0.09864426        -0.067173534
neuronal_up                  0.07027706         -0.02131532         0.238480842          0.38752317         -0.15659472           0.3577991           0.1892366           0.5672812         0.353841822          0.17010487           0.6047937         0.354282079           0.6087488        1.055863e-01           0.1732358           0.4886717         -0.06147035          0.24909699          0.54129393          0.09127180          0.05607375          0.28403989          0.41755055         -0.07975270           0.5899966          0.33505856         0.102693909          0.28051577          0.08310426        -0.006844963         -0.31495393          0.26595406         -0.30096794           0.4279460          0.10930434          -0.2523735         -0.27065562        -0.331425847         -0.04027485         -0.13510844         -0.02925798         -0.13647458         -0.06576075          -0.1651269         -0.23599409          0.08160665        -0.024158946         -0.39125116         -0.08528125         0.242973089
oligodendrocytic_up          0.26340390          0.20728662         0.238562146          0.03463889         -0.23287645           0.1609936           0.1784241           0.2769686        -0.005855304          0.17838346           0.2103914         0.079351508           0.1988334        1.691518e-01           0.1326108           0.2505812         -0.04892868         -0.03712413         -0.06713938          0.01717354          0.34941440          0.14144163         -0.01200277          0.09049891           0.2205388         -0.16470176         0.007669828         -0.08375967         -0.07398330        -0.023669180         -0.06730557          0.04221507         -0.02535599          -0.1434455          0.04683426           0.1519900         -0.01026107         0.006264224         -0.09514740         -0.09808242         -0.10883555         -0.08778694         -0.07144261          -0.1419069          0.01198113         -0.08184800        -0.006479715         -0.04310793          0.03696027        -0.009964341
                    TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up                0.23574567          0.27008722          0.11637555          0.16765565           0.1642266          0.03292988           0.2114207          0.13123819           0.2632937         0.255558714          0.12614825          0.22137032          0.16832484           0.2957996           0.2482320          0.20144142          0.29253731           0.3005284          -0.0101724          0.23305725          0.04509015         0.009178942        -0.001041475           0.2798335          0.03802142         0.055982875          0.10438785          0.05182689          0.10224425          0.05216468           0.0862304          0.02155929        -0.003172836          0.06739361          0.06256693          0.26367322          0.11536744          0.01256467         -0.01613898          0.09388852          0.11605589        -0.022074828          0.01870171           0.1159158          0.06165079           0.1766942          0.16406312           0.1409899           0.1558032           0.1268423
astroglia_up                 0.08497700          0.03829140          0.30608201          0.15711765          -0.1874617         -0.03283596           0.2290560          0.24698566           0.1847376         0.003580519          0.05081910         -0.04184080          0.23607570           0.1738209           0.1859548          0.11158631          0.02925080           0.2737893           0.3973568          0.25676961          0.39896998         0.362511205         0.397819214           0.3570748          0.25126109         0.160334429          0.40718110          0.34688248          0.36362766          0.26827732           0.3482736          0.31181324         0.269671812          0.31453886          0.29877113          0.44352730          0.40788910          0.14601178          0.31162191          0.29587323          0.37947936         0.349232664          0.33243016           0.2628245          0.34952493           0.2376603          0.14605626           0.3990569           0.3289481           0.2267814
neuronal_up                  0.28985543         -0.22610913         -0.06872989         -0.35634904           0.2051659         -0.15883492          -0.1861080         -0.17803520           0.1460343         0.105040208         -0.04944198         -0.33779090          0.29735931          -0.2133380          -0.3174639         -0.16643769         -0.20111679          -0.1413125          -0.1650908          0.01813617         -0.10455488        -0.296484567        -0.187537508           0.2442998         -0.07725316        -0.066574793          0.08146431         -0.06163985         -0.33529820         -0.25395066           0.2275310          0.48981934        -0.150285119         -0.09120100         -0.16014135         -0.01354999         -0.07519059          0.19440942         -0.18040416         -0.21007375         -0.10276626        -0.141371655         -0.21314137          -0.1962376         -0.14976707          -0.1246511         -0.17372631          -0.2207284          -0.1757595           0.1906853
oligodendrocytic_up         -0.04365214         -0.01038323         -0.06776547         -0.08472649          -0.1248816         -0.16991651          -0.1094051         -0.06642471          -0.2030105         0.013242268         -0.01680738         -0.03299205         -0.08840665          -0.2023591          -0.0859446         -0.06875004         -0.09073745           0.4037900          -0.0373881          0.12233991          0.07562161        -0.047601068         0.128217901           0.0132698         -0.15651784         0.007475202         -0.04953692         -0.13635011         -0.02535448         -0.07229950           0.1823742          0.37025576        -0.057417938         -0.06801955         -0.05093462          0.09347360          0.14824246          0.18023574          0.43900131          0.01998225         -0.04886937        -0.003561142          0.12171143           0.2173272          0.20198714          -0.2138286         -0.04280936          -0.1078011           0.2334409           0.1350531
                    TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up               -0.01384884           0.1922211           0.1338636          0.11847725           0.1641095         0.006294324        -0.008137892         -0.13724891           0.2054020          0.12997632          0.01119348          0.05979755           0.1010092          0.08196094          0.06026906        -0.000531532         -0.04216870          0.04782013          0.13415875           0.1741715         -0.04346128         -0.02707061           0.0641008
astroglia_up                 0.25182230           0.2092300           0.3504668          0.38080141           0.3572364         0.285424310         0.266573973          0.21241946           0.3210299          0.26738072          0.31228683          0.39524758           0.3530827          0.36410787          0.42455013         0.259007098          0.19900055          0.21611551          0.25564425           0.4072161          0.27182445          0.30879011           0.2296599
neuronal_up                 -0.21981790          -0.1745162          -0.1645862         -0.16331593          -0.1907196        -0.148526527        -0.150903069         -0.20298432          -0.1494018         -0.31979492         -0.07684811          0.12502843          -0.1325836          0.39917847         -0.26476090         0.306810092         -0.03434656          0.11584141         -0.25353924          -0.1629485         -0.11841551         -0.26324244          -0.1689706
oligodendrocytic_up          0.01801927           0.1762533          -0.1216974         -0.02033394          -0.1266508        -0.086965414         0.006808870         -0.05324112          -0.0283358         -0.08040521         -0.01867919          0.07793677           0.1875986         -0.10327650         -0.02771945         0.087825011         -0.13564146         -0.08870616         -0.02615045          -0.0209192         -0.07626177         -0.05744868           0.1065117
> 
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+                                 grep("_DN$", names(c2BroadSets)))]
> leukPar <- ssgseaParam(leukemia_eset, cgpC2BroadSets,
+                      minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
                                                  CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP                      -0.11212188        -0.09106815       -0.121150864        -0.08143375       -0.088090518        -0.07340947        -0.10376635        -0.12329046       -0.107490316      -0.1094321479        -0.09602253       -0.097841141       -0.052252012       -0.107114347        -0.10907601        -0.07366425        -0.12469120       -0.105311438        -0.11210642        -0.07831097       -0.095506069        -0.09272797       -0.080016602      -0.0601701101       -0.086388455       -0.086143328        -0.07964313        -0.07476053        -0.11573733       -0.106800817        -0.07058489       -0.083557328        -0.08462769       -0.090099523      -0.0549047537       -0.104821669        -0.12270687
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP                      0.12773870         0.11958013        0.169039831         0.08039046        0.079764086         0.04745847         0.17432542         0.10197508        0.108268340       0.2006370201         0.12760627        0.136610607        0.094614756        0.075754012         0.13272714         0.10349286         0.08997838        0.105152129         0.07972599         0.04842713        0.156201488         0.10861902        0.048660863       0.0486013305        0.094428151        0.067025764         0.07166594         0.02581748         0.01906544        0.053825100         0.11114079        0.146989381         0.08036877        0.070876416       0.1065750807        0.032006331         0.03126135
WINTER_HYPOXIA_UP                                         0.19660336         0.22220588        0.208150808         0.20369715        0.194220520         0.18637683         0.18791267         0.18394723        0.191934075       0.2073623135         0.18961007        0.206889571        0.227895816        0.218581670         0.19144735         0.22310948         0.19439608        0.202960622         0.20949776         0.19542339        0.216907511         0.24031950        0.208217532       0.2011029977        0.234533054        0.221475821         0.19919427         0.23800347         0.20715801        0.230102555         0.24544630        0.211888487         0.22075250        0.213354811       0.2209719414        0.212552165         0.19720964
PYEON_HPV_POSITIVE_TUMORS_UP                              0.12936217         0.08608186        0.156095439         0.04512521        0.100883198         0.11208812         0.12352973         0.17187068        0.153348975       0.1703012802         0.11051421        0.170675622        0.015252592        0.094679684         0.14160524         0.08032573         0.13750853        0.138672606         0.08985131         0.03661538        0.105799747         0.08113882        0.107166119       0.0506252281        0.047816290        0.095272447         0.10133515         0.08434566         0.11544536        0.046634453         0.06811758        0.136585794         0.09329885        0.066439827       0.0424873211        0.055346301         0.11044267
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP              0.10497861         0.11810250        0.130550079         0.08824334        0.067996562         0.09001761         0.10880848         0.09112328        0.114928671       0.1341928379         0.11162537        0.121156220        0.097889549        0.134823238         0.11398214         0.10943782         0.10538109        0.110901558         0.10004585         0.07652972        0.124448823         0.09605908        0.095401105       0.0800272992        0.125435027        0.107655114         0.07785774         0.11689738         0.10900193        0.126404590         0.13500916        0.118357443         0.12482627        0.132783820       0.0875660360        0.100749901         0.08896426
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP                 -0.14415962        -0.13112123       -0.148059446        -0.13794539       -0.137336129        -0.12385178        -0.12980927        -0.14141721       -0.145591804      -0.1413958552        -0.11800610       -0.144207294       -0.131972015       -0.141042585        -0.12498393        -0.14357730        -0.12949535       -0.154721081        -0.14240748        -0.12956549       -0.143591188        -0.13236731       -0.149298176      -0.1300145478       -0.131174376       -0.136769869        -0.12031729        -0.13417144        -0.14801656       -0.103740991        -0.11897875       -0.131464086        -0.12259302       -0.128755678      -0.1259053782       -0.135984581        -0.13075821
LU_TUMOR_VASCULATURE_UP                                  -0.08611663        -0.03840696       -0.075208780        -0.06571226       -0.059283399        -0.09743345        -0.01241906        -0.11715637       -0.095094587      -0.0942931758        -0.04907607       -0.091230456       -0.074117889       -0.052525843        -0.06551791        -0.04611678        -0.06288770       -0.095388286        -0.05466379        -0.02196421       -0.089002940        -0.02903084       -0.099934618      -0.0328273529       -0.059930837       -0.093726300        -0.06905892         0.03385055        -0.10159676        0.062777131        -0.04579346       -0.064021288        -0.02096713        0.041382070      -0.0659072134        0.004541717        -0.08085065
KORKOLA_EMBRYONAL_CARCINOMA_UP                            0.14802750         0.19989559        0.193531409         0.19043055        0.164415884         0.14670572         0.13835951         0.15782717        0.158620695       0.1923823767         0.17142120        0.191193516        0.189426831        0.200421860         0.17161690         0.21494495         0.18205192        0.192282258         0.16595727         0.17568860        0.212460788         0.19870684        0.195131434       0.1589439546        0.191376696        0.173976522         0.15799413         0.19036604         0.19127428        0.176196755         0.18543632        0.176852454         0.19522737        0.136840003       0.1714436876        0.171497790         0.18616571
KORKOLA_TERATOMA_UP                                       0.22823416         0.29024180        0.231155370         0.23171935        0.254748989         0.19408563         0.16835792         0.16188829        0.112118254       0.1565428797         0.20383020        0.123476972        0.217612011        0.244082034         0.22362179         0.28040203         0.20831738        0.168287700         0.24110595         0.23418356        0.244983055         0.25692773        0.200311939       0.2184469742        0.248702703        0.190689786         0.21178104         0.22717410         0.21281765        0.198438514         0.21014560        0.161257116         0.19694428        0.158841418       0.2076681127        0.196667083         0.21540144
KORKOLA_YOLK_SAC_TUMOR_UP                                 0.34466298         0.39892106        0.377886303         0.33108088        0.355059703         0.34014296         0.33424236         0.33551668        0.322514107       0.3587143377         0.35616777        0.345656031        0.361905734        0.356409761         0.34356338         0.36466181         0.35676080        0.353135417         0.34782607         0.35557146        0.369519925         0.37855110        0.340752613       0.3310743436        0.310692783        0.333271917         0.33092650         0.35381284         0.34636036        0.330627105         0.35041188        0.339198683         0.36176745        0.298834876       0.3344121129        0.355416500         0.34180114
KORKOLA_CHORIOCARCINOMA_UP                                0.44015614         0.48855227        0.450504964         0.46641488        0.448745786         0.41967427         0.40468719         0.44145971        0.455353414       0.5056625648         0.49198361        0.489745578        0.490534332        0.483410654         0.48684370         0.50623699         0.50398811        0.496025889         0.46027781         0.48204686        0.502594106         0.49342943        0.461528278       0.4453763188        0.453555580        0.457458981         0.44222231         0.48845097         0.47883248        0.485213780         0.48703015        0.459726900         0.46124201        0.434116406       0.4887206089        0.467923068         0.49059426
KORKOLA_SEMINOMA_UP                                       0.13847750         0.17850772        0.174597045         0.16508981        0.157223586         0.15596102         0.14187743         0.14411233        0.155857399       0.1758869779         0.17913681        0.168367099        0.161656280        0.177625715         0.15933775         0.16766991         0.17459358        0.187638049         0.16053712         0.18068610        0.160177064         0.16297719        0.143814313       0.1368714657        0.146708281        0.137036347         0.13672037         0.16405538         0.15687579        0.149515564         0.15499412        0.151293558         0.16531883        0.125764891       0.1551887231        0.172244543         0.16315928
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP         0.27744218         0.26350935        0.297888085         0.25976966        0.276608184         0.25693663         0.27761830         0.28848813        0.286664487       0.2762852086         0.27840239        0.291426599        0.282808179        0.294631962         0.29385340         0.26740892         0.28461746        0.296478631         0.29646299         0.26712951        0.297136943         0.29037251        0.290182379       0.2766321689        0.294832624        0.290120635         0.28546834         0.29985442         0.31836713        0.295872223         0.25619716        0.283982155         0.29792700        0.299964305       0.2675484590        0.301101215         0.29995819
HOLLMAN_APOPTOSIS_VIA_CD40_UP                             0.20838568         0.20620590        0.226021285         0.18903855        0.205996318         0.21204142         0.21967797         0.21308316        0.201127727       0.2021400473         0.20717155        0.215017814        0.187117852        0.219969815         0.21173231         0.19604622         0.21329915        0.212552604         0.19626079         0.19827681        0.211735913         0.19112536        0.203069987       0.2197126547        0.197947624        0.204388551         0.19946042         0.20608121         0.21291368        0.212708378         0.19862400        0.209122222         0.19925121        0.211899137       0.1938569725        0.222442050         0.21241407
LIU_PROSTATE_CANCER_UP                                    0.12333806         0.12822475        0.122836081         0.12725808        0.140594244         0.12825347         0.11034224         0.11649062        0.120184024       0.1301693730         0.12229130        0.129704667        0.137069254        0.111577549         0.11871748         0.11882426         0.12222041        0.139520829         0.11722272         0.12381120        0.128360065         0.13208683        0.142162149       0.1356536483        0.114693190        0.133318936         0.13748781         0.12832984         0.11667838        0.122081679         0.13437113        0.135333521         0.14198109        0.117064049       0.1415429031        0.128631348         0.11727950
LIU_SOX4_TARGETS_UP                                       0.08191204         0.05214134        0.096757396         0.07523797        0.079421912         0.07708861         0.08083627         0.10566201        0.079132766       0.0800895023         0.09502955        0.065630075        0.033165065        0.070986201         0.10605029         0.08258342         0.08768873        0.071996983         0.11390213         0.09018520        0.065872711         0.02685959        0.066144677       0.0727056296        0.082403808        0.073595763         0.06589577         0.06643292         0.09747230        0.106162263         0.04897972        0.066492306         0.06313290        0.112840981       0.0424372639        0.065643621         0.10517315
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP             0.12962537         0.11610080        0.145466087         0.12133965        0.151001465         0.12542172         0.12193757         0.11684710        0.124876198       0.1227735670         0.12962045        0.133337998        0.145216907        0.141828051         0.15001820         0.13815100         0.13460255        0.151878290         0.13727416         0.15746327        0.139912030         0.13476324        0.129655986       0.1284177003        0.132525587        0.130459851         0.12869022         0.13923393         0.13259415        0.155502893         0.13899383        0.126465783         0.14275177        0.146336368       0.1220863251        0.171552323         0.12417440
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP                 -0.04699784        -0.03856334       -0.028301448        -0.03891271       -0.045089149        -0.03704312        -0.02630941        -0.02816459       -0.029559739      -0.0534978383        -0.01366122       -0.041830107       -0.050639545       -0.040411674        -0.02102565        -0.03970615        -0.01799213       -0.033341689        -0.01897268        -0.01365414       -0.028107224        -0.02713442       -0.046683538      -0.0206629560       -0.018977519       -0.038659175        -0.03223894        -0.01494866        -0.02004138        0.028290459        -0.02212699       -0.038100635        -0.02119184        0.003239358      -0.0369081395        0.014342415        -0.01112552
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP                 -0.09394028        -0.10883789       -0.125696986        -0.07648813       -0.114219799        -0.09129576        -0.10820034        -0.09787250       -0.092631165      -0.0637997483        -0.07766220       -0.094268793       -0.082937625       -0.106384923        -0.08192685        -0.10758882        -0.08542658       -0.092203040        -0.06488157        -0.09003358       -0.111067169        -0.08970828       -0.114620536      -0.0850125408       -0.059028109       -0.122409700        -0.11287838        -0.08916244        -0.09472273       -0.077911670        -0.09390619       -0.097644568        -0.11001932       -0.078106059      -0.0940344476       -0.091955745        -0.07766899
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP                      0.02510931         0.08834848        0.080971697         0.01114658        0.025264412         0.04515388         0.06017182         0.06139166       -0.001637575       0.0902450722         0.02735733       -0.004243082        0.008884452        0.024612352         0.02882780         0.04029161         0.10199346       -0.025891095         0.01797175         0.03194774        0.099164270         0.07272077        0.001372288       0.0386279383        0.018516022       -0.003201053         0.04261062         0.04512323         0.05409370        0.082268487        -0.01156691        0.038932474         0.05063402        0.046801355       0.0762341100        0.031483923         0.09146968
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP                      -0.01159980         0.01773789        0.002741870         0.01471238       -0.003972485         0.01295277         0.02605081         0.02748918        0.012317275       0.0001521724         0.01504880        0.002445162        0.026606924        0.001673537         0.04936615        -0.01373036         0.01157459       -0.001213928         0.02950728         0.02709116       -0.001369139         0.01070392       -0.008326614       0.0005865785       -0.006947417        0.003683486         0.01476815         0.00833425        -0.02602648        0.005669794         0.02372157       -0.002592865        -0.01080445        0.018411711      -0.0002326556       -0.019837822        -0.02111218
FRASOR_TAMOXIFEN_RESPONSE_UP                              0.06343555         0.06524186        0.076096149         0.08623646        0.035901095         0.05553414         0.04813651         0.05000595        0.018630799       0.0361654200         0.04294741        0.045994056        0.084165291        0.039521918         0.04147761         0.03215540         0.04010818        0.043314016         0.07676386         0.04559031        0.070087913         0.07091543        0.059398083       0.0706534110        0.071532990        0.068066629         0.06426931         0.07338332         0.08518933        0.065149663         0.07183749        0.066367920         0.06594029        0.077125008       0.0927989288        0.074142612         0.07559066
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP                     0.03004809         0.05432805        0.001432391         0.02459771        0.011252625         0.04038848         0.02972862         0.01314790        0.002092703      -0.0156113936         0.04748579       -0.011117702        0.009640799        0.033918561         0.03840938         0.04608757         0.01172223       -0.005214653         0.03919416         0.04798752       -0.003693506         0.02843361        0.014212574       0.0239450749        0.022041404        0.002291239         0.03366971         0.04054535         0.02752102        0.053112241         0.05954476        0.008942285         0.01327435        0.032914846       0.0378134578        0.024061336         0.01399793
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP                     -0.03953071        -0.05465739       -0.007602480        -0.09969782       -0.064649394        -0.07536982        -0.04164320        -0.05312600       -0.043319892      -0.0119909722        -0.05473042       -0.040898014       -0.087901954       -0.049785859        -0.01812754        -0.08046669        -0.04513855       -0.042191116        -0.06131214        -0.08200335       -0.042998833        -0.05742151       -0.078783092      -0.1056325522       -0.069303843       -0.057059264        -0.07539755        -0.06329446        -0.06679513       -0.049903218        -0.05732776       -0.036949074        -0.04247288       -0.046862641      -0.1023930938       -0.071387634        -0.08894461
WATANABE_COLON_CANCER_MSI_VS_MSS_UP                       0.04819844         0.08558284        0.055708783         0.10324646        0.050709634         0.04995449         0.04822270         0.03763487        0.066913831       0.0260843037         0.03852020        0.041160906        0.092662161        0.050620558         0.03429650         0.05177460         0.08589703        0.046940975         0.04818196         0.04030422        0.077704576         0.10913606        0.057248585       0.0744440801        0.078206610        0.092934179         0.05650890         0.06626172         0.06222949        0.035216390         0.08404366        0.042016648         0.04474503        0.077050552       0.0877448713        0.057929757         0.02811160
> 
> proc.time()
   user  system elapsed 
 63.122   2.104  65.216 

GSVA.Rcheck/tests/test_ssgsea_newapi.Rout.save


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> 
> ## 2023-11-10  axel: simple test script for method ssGSEA, new API
> 
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    expand.grid, I, unname

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db


> library(GSVA)
> 
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
> 
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
> 
> p <- 10000 ## number of genes
> n <- 30    ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+             dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
           s1         s2          s3         s4          s5
g1  1.4171739 -1.3444519 -0.99052898  0.4203395  1.30716224
g2 -0.7281951  0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754  0.09779699 -0.6792548 -0.09124045
g4  1.0735382  1.3156255  0.15588330 -1.8079608  0.48531108
g5  0.7229884 -0.9162342  1.93982245  0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+                    paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> ssgseaPar <- ssgseaParam(X, gs)
> ssgsea.es <- gsva(ssgseaPar, verbose=FALSE)
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
> dim(ssgsea.es)
[1] 100  30
> ssgsea.es[seq.int(min(nRowsToPrint, nrow(ssgsea.es))),]
               s1           s2          s3           s4           s5           s6          s7          s8           s9          s10           s11          s12          s13          s14         s15          s16          s17          s18         s19          s20         s21          s22         s23         s24         s25         s26          s27         s28          s29          s30
gs1   0.050046308  0.153445680  0.06440230  0.245928762 -0.039281351 -0.009166497  0.15513670  0.05825828  0.075703720 0.2211977472  0.1909755963  0.213798011 -0.061198758  0.067211285  0.14116126  0.172193009 -0.076107078  0.146208482  0.27199640  0.027375283  0.25958081 -0.106935451  0.01955332  0.31199267  0.18689996 -0.02538041  0.025160949  0.10202723  0.317960731 -0.077195317
gs2   0.081171485  0.161930448  0.19635614  0.226977722  0.084705475  0.122712065  0.25375216  0.06124718  0.245645786 0.0213152908  0.1553307677  0.123198146  0.188559702  0.090605381  0.13634300  0.045583205  0.117061823  0.170602582  0.25518183  0.162276466  0.09782367  0.004672292  0.14429067  0.23905295  0.15842119  0.17958482  0.278174676  0.12969068  0.012534148  0.036195649
gs3   0.155539308  0.008842632  0.17903935  0.114060106  0.107208758  0.184963019  0.11327060  0.17081118 -0.110611530 0.3187327429  0.0896885519  0.169232189  0.292515661 -0.109522283  0.39211201  0.036070929  0.141878189  0.192157970 -0.01831034 -0.028374783 -0.31739185  0.238016028 -0.06330888  0.16972085  0.38536400  0.19915210  0.020583043  0.25012966  0.186034734  0.232849532
gs4   0.100407452  0.178458402  0.10660518  0.159340098  0.150690547  0.242066049  0.09044728  0.13980211  0.072737831 0.1082857648  0.0915659224  0.136234969  0.061324248  0.115973559  0.28107234  0.138134111  0.214028524  0.086667572  0.09385724 -0.029785545  0.12586634  0.082632971  0.17808866  0.21133946  0.16632346  0.17155219  0.102324377  0.20705832  0.099089588  0.290472119
gs5   0.194033575  0.062793781  0.04848598  0.217341759  0.191914352  0.129512577  0.15090606  0.27146643  0.219627621 0.1165628347  0.1379487730  0.152302042  0.099901051  0.205679023  0.12986947 -0.004963142  0.190709801  0.174401755  0.04427775  0.082055507  0.10896263  0.068825475  0.07614058  0.13558182  0.10568477  0.11492927  0.188047631  0.14065184  0.172431746  0.144376505
gs6   0.025988630  0.233512601  0.04485374  0.149671413  0.164451696  0.223396448  0.13735451  0.15303178  0.125071887 0.2456561342  0.1220311380  0.059904884  0.034633361  0.006225782  0.14294390  0.105914640  0.118989560  0.234603796  0.05542837  0.175273940  0.12454592  0.055488242  0.25878309  0.07422275  0.08197481  0.27581388  0.111785007  0.10024739  0.028180564  0.147366318
gs7   0.121579155  0.248146053  0.20935405  0.098421904  0.005775149  0.141790217 -0.04190763  0.02191384  0.225359966 0.0003605319  0.1938341367  0.218166804  0.234711429  0.171511561  0.14870761  0.004943158  0.168428297  0.131664402  0.16148235  0.046908832  0.09016756  0.199893820  0.17366414  0.10055547  0.08930753  0.16771471  0.141067369  0.20184683  0.113755713  0.062537548
gs8   0.175951236  0.104036859  0.16715411  0.066581368  0.124736570  0.107121162  0.15227018  0.13551209  0.066044097 0.0704654595  0.2006164228  0.164797947  0.149994634  0.063391557  0.20349135  0.205315802  0.006936426  0.130049520  0.17910706  0.061817683  0.05195776  0.059676074  0.18475605  0.10873217  0.25833265 -0.05691274  0.152978263  0.16063583  0.115089785  0.086840652
gs9   0.012967426  0.095461238  0.31825984  0.426422393 -0.206013607 -0.324946275  0.08738730 -0.14420537  0.061606991 0.1058375433  0.3407494698  0.060782012  0.036354426  0.158643593  0.02660000  0.070018029  0.295526014  0.370485869  0.31177819 -0.048490861  0.14293901 -0.052155641  0.39443397  0.18784912 -0.02491664  0.42956908  0.004366843 -0.09351215  0.539660825  0.194470958
gs10  0.310450557 -0.155381634 -0.04662343  0.069903089  0.235460838  0.136094565  0.35534293  0.14451145  0.032811542 0.2783927322 -0.0003708892  0.364801135  0.085153930 -0.007025257  0.31541487  0.214116068  0.076379415  0.300464786  0.02436326  0.014174550  0.29010030  0.353773500 -0.14036272  0.31414362  0.07517937 -0.36240056  0.135363804 -0.03291463  0.153638245 -0.006111044
gs11  0.148113831  0.288039198 -0.01173447 -0.125211500  0.422877496  0.368992470  0.31511056  0.11703945  0.119067901 0.2969431165  0.1767112563  0.269003140 -0.126699232  0.063371585 -0.15584600 -0.181509478 -0.252102260  0.084592131  0.41484382  0.102741674  0.19038088  0.155665264  0.11205065  0.18151841  0.07962262 -0.12707952 -0.043348625  0.52382483  0.471772841  0.192133037
gs12  0.191362265  0.075821020  0.10101534  0.015589766  0.118539915  0.150230064  0.11740963  0.09874133  0.196307720 0.1336100372  0.2243542624 -0.037860476  0.035827902  0.019570602  0.05739397 -0.086404343  0.090407547  0.090844017  0.11188849  0.250652019  0.15642076  0.100960304  0.13217523  0.09147595  0.14935140  0.07679723  0.164747489  0.10884565  0.021875796  0.224835781
gs13  0.291858703  0.346475308  0.21825672  0.130219327 -0.045991328  0.234867271  0.34027295  0.11127727  0.246617815 0.3200429439  0.0493766799  0.008390396  0.100929397 -0.036222987  0.09552925  0.116070504  0.050409473  0.117373720  0.33645267  0.196460577  0.28151964  0.250645402  0.00786962  0.16471272  0.26987750  0.14003078  0.274510723 -0.06972362  0.111250445  0.031727494
gs14  0.190335262 -0.064441167 -0.14720764  0.313073121  0.184851969  0.034311372  0.29316721 -0.12497882  0.099774835 0.0064937265  0.1376061089  0.105283947  0.322046351  0.260972829  0.22468693  0.113901307  0.002316888  0.174550489  0.03848764  0.149291379  0.16606614  0.171358521 -0.23264680  0.06333781  0.26046384  0.14647155  0.061583955  0.07893101  0.084042439  0.241795872
gs15  0.217913642  0.141978343  0.21703088  0.061088530  0.048906153  0.109096881  0.04362714  0.21225573  0.180978230 0.1203085545  0.0888328589  0.183656898  0.074251458  0.108846516  0.01790968  0.222984303  0.115016738  0.124120115  0.11555410  0.162960343  0.12134445  0.108547160  0.18775900  0.20267430  0.21813681  0.05956895  0.081086983  0.04401661  0.004584748  0.113053205
gs16  0.008372193  0.198823477  0.02924146  0.187858615  0.054689339  0.068398317  0.10730408  0.05120743  0.070935563 0.0784796201  0.0060339391  0.097386464  0.181367848  0.060028026  0.18405253  0.129145564  0.127244708  0.083034338  0.06835057  0.111075315  0.12519485  0.101386193  0.10027865  0.07630206  0.11786623  0.12151097  0.076099407  0.06340149  0.199302468  0.107472386
gs17 -0.021209113  0.041234441  0.15849782  0.140830687  0.094989136  0.050310553  0.27875609  0.19671686  0.224090634 0.0823059119  0.1446622842  0.073610528  0.181135843  0.128995630  0.18515033  0.043619934  0.156832276  0.139817243  0.12097998  0.094078972 -0.01250999  0.263313353  0.18157262  0.06476920 -0.02611791  0.19436554  0.098776218  0.15857389  0.086521226  0.140174046
gs18  0.224221766  0.208703330  0.19566999  0.277362679  0.086022967  0.155782407  0.21984017  0.06224476  0.184311430 0.0746810884  0.1500112520  0.031591001  0.218220154  0.085782290  0.05403013  0.239733411  0.225608272  0.080410483  0.12419147  0.087988742  0.09109210  0.118154979  0.18042347  0.15034333  0.05419059  0.06131728  0.135992696  0.05116987  0.008007108  0.258350779
gs19  0.060496086  0.192359984  0.06580294  0.039342129  0.056421351 -0.050071255  0.09835605  0.19838255  0.232365057 0.1878213634  0.0597175977  0.113955441  0.138654652  0.118112400  0.02948580  0.183873151  0.295382463  0.084940527  0.01555718  0.237711415  0.15405004  0.113893226  0.01261294  0.08150703  0.13679835  0.17664342  0.264724147  0.09871800  0.219093664  0.229287431
gs20 -0.002331868  0.104835345  0.19095558  0.196525176  0.230511428  0.196485997  0.20691704  0.06292261  0.195484717 0.0748935120  0.2274655731  0.234958644  0.100720547  0.098787011  0.01322616  0.215826190  0.107383744  0.272734953  0.14006653  0.128606660  0.17526232  0.154071267  0.20185690  0.16029505  0.11767405  0.04019989  0.087560954  0.12297014  0.120555888  0.165784444
gs21  0.235531812  0.174101071  0.04331386  0.066700909  0.161550174  0.127508845  0.22978825  0.07748909  0.142407170 0.1262273951  0.0698341132  0.023900707  0.157264078  0.064306708  0.19037040  0.022272735  0.085059711 -0.030333898  0.10370986  0.041024634  0.15543738  0.156630569  0.11755610  0.14827641  0.09418257  0.26082349  0.175064303  0.10818015  0.134571164  0.137789233
gs22 -0.047650929  0.186841315  0.03222656  0.119471610  0.193877261 -0.031790084  0.29277495  0.07689763 -0.019411157 0.0595495594  0.3807452330  0.071668171  0.135528037  0.177342300  0.18766862  0.143986114  0.138391599  0.137573467  0.11420368  0.222882426  0.06096151  0.160136193  0.37542340  0.34681913  0.02224170  0.20670334  0.053159207  0.38290841  0.093613064  0.168206100
gs23  0.144199311  0.186850465  0.09563174  0.191503633  0.197926948  0.183687676  0.08857992  0.08438396 -0.002354026 0.1015861893  0.1556606664  0.149031544 -0.003876439  0.220881227  0.19108193  0.128779302  0.115583034  0.128810013  0.21233978 -0.001768056  0.13275623  0.154387029 -0.06742232  0.07991395  0.15197278  0.23716849  0.161038324  0.06541124  0.045781546  0.096529440
gs24  0.244519906  0.255495479 -0.02212643  0.007561398  0.045577309 -0.009892961 -0.04971968  0.19698687 -0.078933887 0.0414502136  0.3742714753 -0.050544352  0.013590683  0.003608241 -0.34825490  0.415098155  0.138025957 -0.001864139 -0.37016901  0.117420895  0.37252626 -0.116751635  0.32072205 -0.06702968  0.11533867  0.21077948 -0.041474525  0.03217032 -0.044872621  0.165434542
gs25  0.193601681  0.091245208  0.18463093  0.100724310  0.055381436  0.002669872  0.08514397  0.05620041  0.124029775 0.1800670374  0.1742834586  0.170840558 -0.034319609  0.177918537  0.09381717  0.145284931  0.208953543  0.324830001  0.16350519  0.037554150  0.26681356  0.012083285  0.28774452  0.13816374  0.05451236  0.10453580  0.280375699  0.12512785  0.135834785 -0.038267879
> 
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+                     featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+                     sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+                                       grep("^REACTOME", names(c2BroadSets)),
+                                       grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- ssgseaParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+                       minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
                                                    NA19099      NA18523     NA19144     NA19137      NA18861     NA19116     NA19130       NA19131      NA19119     NA19152     NA19153      NA19140     NA19138     NA18522     NA19192     NA19193     NA19239       NA19238      NA19210     NA19201     NA19172      NA18870     NA18858     NA18852      NA19159      NA18855     NA19204      NA18501      NA19127      NA19098      NA19093      NA18856     NA18912     NA18517     NA18502      NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                  0.21698978  0.190101718  0.20525435  0.21623854  0.228779757  0.20936853  0.22506971  0.2234235687  0.220780261  0.21444921  0.21903592  0.220664804  0.20924941  0.21012248  0.20502111  0.19985724  0.19721755  0.1913957094  0.225134348  0.21709921  0.20425590  0.201712948  0.19379346  0.23122161  0.221525326  0.212463371  0.22792181  0.221128254  0.204351144  0.218947974  0.222579602  0.229420498  0.22060750  0.20299621  0.21904369  0.215493102
KEGG_CITRATE_CYCLE_TCA_CYCLE                     0.32433043  0.330666662  0.31869186  0.30766734  0.322670342  0.31519248  0.31986814  0.3185006606  0.329706974  0.31265435  0.32676917  0.331734849  0.31520463  0.32288700  0.31043279  0.31220717  0.30722070  0.3168181879  0.320522995  0.32920820  0.31023554  0.313528956  0.32324416  0.32442285  0.307746225  0.302000352  0.31422539  0.325061712  0.324433443  0.320805701  0.313120479  0.322340322  0.32303440  0.31470507  0.32982874  0.322774682
KEGG_PENTOSE_PHOSPHATE_PATHWAY                   0.32613456  0.292246085  0.32171779  0.31922331  0.327342371  0.32285413  0.31703691  0.3267972444  0.317799481  0.30548746  0.32071494  0.325200548  0.31574521  0.32222525  0.30445849  0.31198274  0.30056356  0.3175363433  0.313248908  0.31537383  0.31498239  0.312138133  0.31157241  0.31348063  0.313260085  0.305543436  0.31306655  0.318602720  0.309415331  0.316959102  0.307805386  0.319474001  0.30318847  0.31470071  0.31941053  0.326759498
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS    0.14142675  0.152207936  0.14238572  0.07942752  0.105050011  0.12961280  0.11296245  0.1601888948  0.141345242  0.09869492  0.16412075  0.158434716  0.10823031  0.17672793  0.13428568  0.11392145  0.14170168  0.1428868433  0.146955737  0.14818936  0.17164951  0.138839694  0.12229281  0.11673825  0.109550600  0.069456602  0.14040696  0.182050959  0.114699787  0.189319064  0.130300608  0.111638487  0.14391952  0.12318954  0.12224946  0.137976483
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM             0.15550203  0.118146628  0.14707933  0.18705703  0.199943713  0.16410186  0.16813615  0.1802125060  0.170259262  0.18671240  0.18252531  0.164279928  0.16794179  0.17149276  0.16625970  0.14528892  0.13398404  0.1378452121  0.169092878  0.19220147  0.19047757  0.157694632  0.12722729  0.18630354  0.195343439  0.176599720  0.19802720  0.161573744  0.152184181  0.173797461  0.187295272  0.197591583  0.17232864  0.16136207  0.17911558  0.180031024
KEGG_GALACTOSE_METABOLISM                        0.11149473  0.103217880  0.11085844  0.13741766  0.165952026  0.14418332  0.12726683  0.1370210459  0.142805283  0.15242781  0.15221252  0.149682255  0.15018345  0.14626213  0.11999955  0.11557928  0.11593006  0.1148701557  0.149672283  0.16891575  0.16494312  0.123919369  0.09211866  0.14937665  0.176575543  0.129061875  0.17075453  0.137859374  0.112830567  0.139888692  0.144650768  0.159081145  0.13428014  0.12448791  0.15631215  0.169827420
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM           0.04198555 -0.032292278  0.01406413 -0.01064716 -0.022308338 -0.03194340 -0.01037135  0.0661161558 -0.007360627 -0.02923521  0.01141517  0.001497673 -0.01420985  0.03438381 -0.03203514 -0.01804054 -0.01538922 -0.0026678425  0.027398691 -0.04882214 -0.11561188 -0.008509357 -0.01203473 -0.02089645  0.001083068 -0.003061739 -0.11355468  0.027193644 -0.020507654  0.050375480  0.023851383  0.004333629  0.02757450 -0.01461678 -0.01931510  0.006947649
KEGG_FATTY_ACID_METABOLISM                       0.19144010  0.177618186  0.19229237  0.18162156  0.195013260  0.17285053  0.18737923  0.2094263692  0.189298006  0.17744684  0.17726086  0.187594417  0.17484769  0.18064373  0.17580318  0.16279037  0.17715535  0.1847771315  0.187298535  0.17615351  0.15131681  0.184344838  0.17544154  0.18540490  0.164558082  0.179209973  0.15666232  0.189591897  0.183358359  0.189661362  0.185937924  0.195641028  0.20399213  0.18301653  0.17977089  0.185912168
KEGG_STEROID_BIOSYNTHESIS                        0.29508326  0.295486909  0.26286536  0.27906495  0.291220515  0.28574075  0.30491564  0.3028446031  0.306065643  0.26781522  0.29464863  0.281727962  0.28372727  0.30309918  0.30917324  0.26593252  0.26945212  0.3018824439  0.272449306  0.28920242  0.27852421  0.273019343  0.28299044  0.28594314  0.297497744  0.264419747  0.26785147  0.276188961  0.286487520  0.308034927  0.289095316  0.299848680  0.29269188  0.29943769  0.29468427  0.287313424
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS             -0.03581753 -0.092130799 -0.04761225  0.05891582 -0.123502963 -0.08482548 -0.02276997 -0.0448787260 -0.064166255 -0.15073085 -0.07715570 -0.027840150 -0.03137614 -0.08997226 -0.12858747 -0.15452411 -0.15192399 -0.0008490506 -0.141927194 -0.12439918 -0.14957231 -0.052218742 -0.06096819 -0.03648457 -0.146524551 -0.129025468 -0.15339387  0.017340701  0.013213935  0.021006051 -0.008592746 -0.079442545 -0.01531376 -0.09542512 -0.12181560 -0.100962579
KEGG_STEROID_HORMONE_BIOSYNTHESIS               -0.00603142 -0.048459074 -0.07974466 -0.01648330 -0.091376743 -0.04645294 -0.05783215 -0.0077100648 -0.032440674 -0.04925962  0.01257962 -0.027085733 -0.05133063 -0.03464357 -0.09107591 -0.04604528 -0.06313163 -0.0037229305 -0.083744196 -0.04403506 -0.07403528 -0.041751578 -0.06718897 -0.06224135 -0.022813686 -0.063619976 -0.05046193 -0.046775240 -0.007732293 -0.031014587  0.038972593 -0.058183774  0.01398730 -0.04158946 -0.10044713 -0.022828144
KEGG_OXIDATIVE_PHOSPHORYLATION                   0.23470278  0.265724094  0.26337583  0.24721506  0.255184437  0.25137871  0.25453660  0.2566994039  0.246493165  0.25745496  0.25786805  0.247495875  0.25321032  0.26043249  0.24844391  0.24615206  0.25180784  0.2621473829  0.253121007  0.24466091  0.24444401  0.248324354  0.24596943  0.26085564  0.252493166  0.259461341  0.25704694  0.244689333  0.244937049  0.247126050  0.249275632  0.253150955  0.25606696  0.26126201  0.26134069  0.248688913
KEGG_PURINE_METABOLISM                           0.11282696  0.113448858  0.13052367  0.12872555  0.130498773  0.12514834  0.12708974  0.1254518508  0.114374092  0.11746139  0.12720504  0.123909976  0.12501986  0.12926543  0.11864833  0.11039303  0.11837407  0.1306561048  0.120874877  0.11874917  0.12461513  0.118754355  0.11004336  0.12341313  0.111728921  0.125220817  0.12599093  0.120422095  0.116669899  0.120942649  0.125716426  0.120651681  0.12066825  0.12286847  0.11781015  0.119089666
KEGG_PYRIMIDINE_METABOLISM                       0.17757771  0.175394817  0.19858724  0.19679890  0.184451412  0.18857531  0.19443581  0.1913521689  0.176616057  0.18757690  0.18742386  0.190866974  0.17707165  0.19343157  0.18609589  0.18058113  0.18517942  0.1962563816  0.174386960  0.18912297  0.18783617  0.175188077  0.17750981  0.19040712  0.177216013  0.198853296  0.18467609  0.173153515  0.179616517  0.173598395  0.177726615  0.185542608  0.19263573  0.19211082  0.17683259  0.184513099
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM  0.10989042  0.093058240  0.09075182  0.09975330  0.110553924  0.08932985  0.10833717  0.1022932484  0.098714538  0.09452201  0.10412503  0.112821342  0.09845573  0.09864529  0.10839464  0.10195788  0.09460140  0.0890330658  0.114926416  0.12373452  0.09891343  0.096051085  0.08806549  0.11101748  0.101678482  0.090367626  0.10014984  0.113927079  0.088757290  0.111944663  0.101911619  0.091610295  0.08631087  0.10449490  0.09680798  0.113666733
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM     0.07589995  0.013164475  0.03073650  0.05497730  0.075187517  0.04629436  0.05684194  0.0721291176  0.091914474  0.05519977  0.08746496  0.050067541  0.05965801  0.06067566  0.08409397  0.10238484  0.01501362  0.0045650662  0.049144983  0.07054669  0.05116744  0.045186268  0.05137738  0.06424885  0.085465393  0.053004029  0.06129235  0.050492310  0.064513199  0.069147728  0.067789023  0.075006091  0.03311465  0.05179666  0.09353812  0.069833588
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM          0.25896290  0.229197097  0.23915083  0.24454874  0.251021905  0.23616587  0.24671301  0.2542987322  0.256828445  0.24146968  0.26145521  0.245522688  0.24379502  0.24900959  0.26862910  0.25530625  0.22947514  0.2349385424  0.237967026  0.24111547  0.26557949  0.234639477  0.23412745  0.23301781  0.258395796  0.215746987  0.23465476  0.256687996  0.239987950  0.250370070  0.237026241  0.252743721  0.22651684  0.23865720  0.25741554  0.244270299
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION   0.18843747  0.186649426  0.17530857  0.15633381  0.178282757  0.18033157  0.18581500  0.1963894497  0.191659866  0.14190172  0.20151595  0.181514394  0.18800238  0.18208434  0.18884446  0.17012565  0.16953990  0.1676338847  0.183699227  0.19745711  0.16337494  0.161194552  0.15788716  0.18351104  0.171161284  0.163754665  0.15047991  0.196948812  0.185610694  0.198192986  0.174172878  0.182779264  0.17802037  0.16062757  0.19890618  0.189941640
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS  0.28568183  0.282786776  0.24961716  0.24491634  0.270528716  0.29605800  0.25836996  0.2521218808  0.281679472  0.24721670  0.32053768  0.274690843  0.28302481  0.30038542  0.30322093  0.29120270  0.28253548  0.2579537498  0.267208046  0.32453395  0.29189041  0.267396603  0.24747811  0.28281020  0.293967599  0.262178623  0.29429367  0.269346291  0.263428379  0.266865452  0.261098171  0.251262879  0.25119395  0.28412517  0.31296991  0.299112229
KEGG_LYSINE_DEGRADATION                          0.11363066  0.093971946  0.11756645  0.11921555  0.114150109  0.11417055  0.11382771  0.1282543770  0.110373515  0.10264637  0.10896281  0.119922709  0.11111424  0.09923486  0.10398550  0.09158226  0.11014421  0.0992105519  0.114396655  0.11105307  0.10519398  0.095412052  0.09666140  0.10310679  0.108674463  0.114399506  0.09091906  0.108210445  0.111356587  0.117142092  0.103818204  0.110313192  0.10414576  0.09228489  0.10733176  0.111914878
KEGG_ARGININE_AND_PROLINE_METABOLISM             0.12738384  0.120646580  0.12800721  0.12780121  0.140190182  0.11234716  0.13886310  0.1363147983  0.118339180  0.12495239  0.13387648  0.119717717  0.12674429  0.11413969  0.12760775  0.12051016  0.11112441  0.1060723468  0.135207120  0.11384185  0.11270554  0.120444480  0.10890719  0.13671193  0.148306216  0.127590175  0.12033740  0.129990177  0.120085884  0.143513369  0.139267799  0.139711646  0.12631236  0.12302536  0.13671696  0.129915338
KEGG_HISTIDINE_METABOLISM                        0.01037506 -0.009232361 -0.02503732 -0.04007054 -0.004116879 -0.02891744 -0.02515002  0.0005514458 -0.015393247 -0.03216059 -0.03701174 -0.018066447 -0.04417577 -0.03579879 -0.02417860 -0.02971581 -0.02648223 -0.0314952886  0.009196744 -0.04701498 -0.06879069 -0.022838496 -0.03099772 -0.03704899 -0.025519728 -0.039940345 -0.08649494  0.003895911 -0.029842438 -0.000484478 -0.020239498 -0.027308388 -0.01132841 -0.03055363 -0.02153193 -0.036015417
KEGG_TYROSINE_METABOLISM                         0.06714488  0.053002829  0.05753161  0.04337986  0.057065867  0.05794194  0.05847814  0.0507298323  0.058615853  0.04701795  0.05759954  0.046542561  0.04954693  0.06556692  0.07181820  0.05370509  0.05763770  0.0690302934  0.044285470  0.04352433  0.06313789  0.067191326  0.04882973  0.05342728  0.052557681  0.041207045  0.04378767  0.064256091  0.055186897  0.048349590  0.069931678  0.042623088  0.06573735  0.06531103  0.05853359  0.057231880
KEGG_PHENYLALANINE_METABOLISM                    0.11960304  0.096377593  0.09464200  0.09061793  0.091267769  0.09170094  0.09990226  0.0976280231  0.105007097  0.08739764  0.09597757  0.092011591  0.10469452  0.09925149  0.10437604  0.10710066  0.07942615  0.0989797292  0.119065427  0.09925727  0.10453704  0.086330586  0.09687302  0.10521245  0.097635425  0.085996013  0.09971671  0.107245185  0.084152959  0.091621331  0.102207053  0.107399793  0.10262963  0.09509872  0.08816275  0.098383108
KEGG_TRYPTOPHAN_METABOLISM                       0.12707074  0.135904404  0.12002196  0.10198472  0.105456181  0.10258554  0.11263398  0.1471089408  0.134184467  0.09404104  0.12387419  0.114507791  0.10212085  0.12955711  0.09526545  0.11899775  0.10760770  0.1237862285  0.125934177  0.11873044  0.06658891  0.112588368  0.11212948  0.10011186  0.118024833  0.113614802  0.09153418  0.132524487  0.110393708  0.120368868  0.125229509  0.116181945  0.14682099  0.11978502  0.10429972  0.118580441
> pickrellPar <- ssgseaParam(pickrellCountsArgonneCQNcommon_eset,
+                          canonicalC2BroadSets, minSize=5, maxSize=500)
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
> exprs(esrnaseq[seq.int(min(nRowsToPrint, nrow(esrnaseq))),])
                                                     NA19099      NA18523     NA19144     NA19137     NA18861     NA19116     NA19130     NA19131     NA19119     NA19152      NA19153     NA19140      NA19138     NA18522     NA19192      NA19193     NA19239      NA19238     NA19210     NA19201     NA19172     NA18870     NA18858      NA18852      NA19159      NA18855     NA19204     NA18501       NA19127     NA19098     NA19093     NA18856     NA18912     NA18517     NA18502     NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                  0.256075759  0.234440285  0.22365541  0.25164814  0.25617134  0.22440002  0.26825331  0.24363221  0.22303626  0.24453749  0.241659658  0.24784931  0.240912314  0.26440850  0.25175671  0.221994177  0.25951673  0.257749187  0.23737636  0.23373922  0.24102923  0.24394811  0.24421325  0.253552534  0.230189600  0.233117341  0.25308269  0.25087262  2.352772e-01  0.25308477  0.25405537  0.23991583  0.23478740  0.24563546  0.25646515  0.25071702
KEGG_CITRATE_CYCLE_TCA_CYCLE                     0.276806659  0.263840724  0.24698443  0.27529933  0.27555689  0.24975236  0.28827170  0.26740093  0.22453250  0.25824366  0.264578233  0.26626941  0.267999750  0.27293682  0.26955574  0.218915231  0.28141656  0.274122454  0.25380024  0.25929889  0.26072040  0.26865139  0.27076349  0.265378539  0.244259988  0.241425821  0.28531051  0.28111746  2.409079e-01  0.26208495  0.26235839  0.27393384  0.25428617  0.26899433  0.27380231  0.26464529
KEGG_PENTOSE_PHOSPHATE_PATHWAY                   0.308157944  0.298087515  0.29014344  0.31316947  0.31075726  0.29580575  0.33150923  0.30911766  0.27215128  0.29310006  0.318390367  0.31750877  0.303315781  0.32990830  0.31603865  0.276156993  0.32137928  0.328904420  0.28873356  0.28984710  0.29765756  0.29417757  0.30408635  0.309010795  0.284366223  0.286933996  0.32289659  0.31674788  2.939716e-01  0.30287805  0.30290168  0.30124596  0.29981504  0.30880460  0.29585316  0.31112043
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS    0.072900627  0.058114116  0.05095095  0.05552091  0.06878391  0.07768438  0.08213775  0.09250688  0.03556826  0.09156620  0.097878249  0.06956272  0.081520495  0.14591883  0.10114649  0.031874974  0.09204189  0.115726730  0.08879480  0.08133511  0.11303741  0.04597980  0.05930134  0.091652196  0.045442518  0.015179733  0.11243384  0.13618849  5.819542e-02  0.07901269  0.10767281  0.06217197  0.10083457  0.07884946  0.04823275  0.08069438
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM             0.179143833  0.181466412  0.18164218  0.20648051  0.16508263  0.15692126  0.20526979  0.18220460  0.12828973  0.18948921  0.194624757  0.18678502  0.191651374  0.18621396  0.21686165  0.163982758  0.20153270  0.213681011  0.17124101  0.18326784  0.17747109  0.18055651  0.18666452  0.208603904  0.182698854  0.186529878  0.20249678  0.14324407  1.692164e-01  0.17589451  0.20061610  0.16286430  0.16195031  0.19908025  0.18482874  0.20501174
KEGG_GALACTOSE_METABOLISM                        0.181131627  0.159926813  0.16270579  0.20573093  0.18044266  0.15543518  0.21952142  0.17843456  0.12359001  0.18349838  0.199111340  0.19452033  0.190574177  0.19551040  0.22253670  0.149654098  0.20567552  0.200581366  0.17030505  0.18223148  0.18954484  0.17613758  0.17006314  0.194920826  0.198422033  0.192448054  0.22245521  0.15408689  1.635711e-01  0.17252060  0.20589447  0.15895753  0.15412635  0.18901486  0.18924635  0.20842567
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM           0.076244940  0.080303827  0.01896975  0.05351930  0.05634166  0.03667802  0.08143338  0.05261833  0.02095408  0.09594147  0.046490176  0.03601321  0.072687156  0.13959149  0.04107588  0.001557203  0.08580840  0.109000508  0.05530623  0.01833645 -0.08023056  0.01932496  0.06300957  0.066003820  0.023771292  0.007102489  0.03086936  0.10270298 -3.157042e-03  0.05314639  0.07495172  0.08280269  0.05626948  0.04257381  0.06298584  0.07433531
KEGG_FATTY_ACID_METABOLISM                       0.189817509  0.170872559  0.14155879  0.19190458  0.20061758  0.16220943  0.20719303  0.18088378  0.16687336  0.17684223  0.169286125  0.17914218  0.178915532  0.20998722  0.17201976  0.131109962  0.20936840  0.197325741  0.16514248  0.15827116  0.16387239  0.17860585  0.18319739  0.188238171  0.113651303  0.130750066  0.17770022  0.19465482  1.597647e-01  0.18876629  0.18911247  0.18967056  0.15979790  0.16688397  0.17911784  0.19754478
KEGG_STEROID_BIOSYNTHESIS                        0.224283008  0.183502868  0.10641865  0.15431521  0.20673953  0.19381572  0.19919988  0.19375955  0.13759180  0.13279097  0.166353748  0.15479731  0.201859944  0.18441257  0.20240525  0.138935955  0.16161930  0.187730965  0.12780607  0.17277089  0.17211107  0.17687687  0.20523660  0.178291553  0.222139792  0.187421826  0.17910855  0.15862534  1.563029e-01  0.17970860  0.21186843  0.18641454  0.20553433  0.21995063  0.24238713  0.17376305
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS              0.007298097 -0.045231480 -0.05615631  0.07155428 -0.03778360 -0.06475813 -0.01631200 -0.01120530 -0.07059793 -0.07173726 -0.040573532 -0.01433368  0.005000649  0.05037597 -0.04733764 -0.070668142 -0.04251391 -0.016724966 -0.03493901 -0.06316513 -0.04576571 -0.03089320 -0.02209954 -0.003440324 -0.082490284 -0.065017438 -0.04750185 -0.03693552 -2.405233e-05  0.03741013  0.04625340 -0.02630856 -0.04838299 -0.05724028 -0.04066866 -0.03635462
KEGG_STEROID_HORMONE_BIOSYNTHESIS               -0.046018108 -0.093294319 -0.13746745 -0.05837140 -0.11437771 -0.04362896 -0.07770349 -0.07282807 -0.09993655 -0.05986338 -0.051748220 -0.07057083 -0.081288974 -0.04819890 -0.08749854 -0.080358972 -0.09355664 -0.072350610 -0.13131875 -0.06410751 -0.13561358 -0.09017416 -0.11589119 -0.085631744 -0.094304978 -0.119555451 -0.07166260 -0.03448379 -6.616326e-02 -0.10521967  0.02700273 -0.04856765 -0.05304776 -0.11560595 -0.12890981 -0.06549103
KEGG_OXIDATIVE_PHOSPHORYLATION                   0.290044085  0.306375054  0.26041452  0.29564165  0.29454677  0.28682961  0.31516942  0.29225539  0.29624881  0.28190329  0.288965873  0.29838803  0.296122751  0.30714929  0.29408922  0.298005863  0.29592505  0.304180875  0.28081795  0.28727692  0.29838136  0.30109527  0.29148313  0.294331078  0.252378384  0.264546548  0.29654867  0.30641064  3.067693e-01  0.28941630  0.30210492  0.30197862  0.31189519  0.28625608  0.28901836  0.28725201
KEGG_PURINE_METABOLISM                           0.121552424  0.114160233  0.11048165  0.13105255  0.11833540  0.10870679  0.12953106  0.12047921  0.08446782  0.11231713  0.112887563  0.11536146  0.105467789  0.13155054  0.12002126  0.113011238  0.12896358  0.123095976  0.11982023  0.10583172  0.10912082  0.11113234  0.10512995  0.109356079  0.099193918  0.103015548  0.12720303  0.13748276  1.143107e-01  0.12051435  0.10972889  0.11378580  0.10276405  0.11768950  0.10730690  0.11186763
KEGG_PYRIMIDINE_METABOLISM                       0.159729043  0.145500125  0.14730788  0.17410916  0.15340765  0.14791645  0.16855838  0.15892991  0.11381615  0.15157687  0.147076658  0.15194721  0.127133366  0.17182833  0.15867282  0.142850963  0.16307797  0.161493787  0.14783129  0.14154301  0.14666943  0.14191003  0.14540419  0.146472588  0.114588161  0.131180250  0.16581516  0.18090777  1.515887e-01  0.16056284  0.13622778  0.16268189  0.13979801  0.15559869  0.13630535  0.15387683
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM  0.112712342  0.074567957  0.08695191  0.09240285  0.11298142  0.09506027  0.09739823  0.07764648  0.10950728  0.07593407  0.076879433  0.07931452  0.081605261  0.10786533  0.09769440  0.046974792  0.08948356  0.076841077  0.09165978  0.07828511  0.07203344  0.08737763  0.06590033  0.087495399  0.073193496  0.070563832  0.10778181  0.09237847  6.349400e-02  0.12215027  0.08568016  0.06775927  0.05945302  0.08035606  0.08620309  0.09688249
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM     0.063414089  0.008780948  0.05935336  0.06694159  0.06788012  0.04426421  0.03357666  0.04745672  0.07210759  0.05011682  0.019676287  0.05273708  0.007465601  0.07973086  0.04674425  0.006592034  0.03645575  0.007696429  0.06004590  0.01417259 -0.02089575  0.04782863  0.03721318  0.033513757  0.059026917  0.026399449  0.05354070 -0.01859829  3.487693e-02  0.09841955  0.03620653  0.02255710 -0.01427914  0.03857687  0.09608318  0.07059776
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM          0.234037901  0.189794344  0.20539118  0.22853483  0.22730123  0.19920525  0.19855436  0.22105176  0.21859510  0.21569681  0.192366034  0.19664087  0.202877108  0.24438081  0.22600833  0.162641803  0.19791966  0.190679930  0.19704281  0.18167020  0.20854176  0.21380744  0.20125670  0.201679421  0.212128486  0.203347274  0.19742841  0.19425738  1.833991e-01  0.22861206  0.18710448  0.20444733  0.17838357  0.19817716  0.21897475  0.22036231
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION   0.149779799  0.130868968  0.11141194  0.15213162  0.15707673  0.12253970  0.17713191  0.13281221  0.14628124  0.12815576  0.154689122  0.13889347  0.148455429  0.18582753  0.14490882  0.100438410  0.16119649  0.158609790  0.12845278  0.13377880  0.12834048  0.13474814  0.13427088  0.163849429  0.097733032  0.107920307  0.15085656  0.15995811  1.171796e-01  0.15812798  0.14524879  0.14585176  0.13929386  0.12933917  0.15265580  0.15760441
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS  0.295088488  0.261790244  0.20437749  0.28756505  0.29611186  0.27215510  0.27635622  0.24614956  0.27920993  0.21961975  0.291130821  0.26258549  0.257402155  0.29814324  0.28934456  0.233740001  0.27822280  0.256193143  0.24326695  0.27454545  0.27722539  0.24789039  0.23212598  0.282819863  0.269379426  0.251031182  0.30807137  0.28499798  2.550574e-01  0.27349722  0.26662427  0.24049639  0.27670544  0.24397409  0.28271525  0.28462182
KEGG_LYSINE_DEGRADATION                          0.141718140  0.125418015  0.13297959  0.14283107  0.13473057  0.12203529  0.14719941  0.13385750  0.09491781  0.12236495  0.122241586  0.12711931  0.124884910  0.13829366  0.13755243  0.119698191  0.14226579  0.133886134  0.14436915  0.11175177  0.10560139  0.13083694  0.13813000  0.135265809  0.112781050  0.123216658  0.12973261  0.13564156  1.232322e-01  0.13580749  0.12462139  0.13626539  0.10525941  0.13533806  0.13567788  0.14158147
KEGG_ARGININE_AND_PROLINE_METABOLISM             0.135734485  0.123178563  0.10586472  0.12564409  0.14906498  0.11818042  0.14021365  0.12277557  0.09432899  0.11770248  0.140202156  0.10961800  0.124468602  0.13170402  0.12160081  0.090198152  0.12999175  0.127112384  0.11788380  0.11428458  0.11762968  0.13710845  0.11356352  0.130539368  0.104547379  0.117760260  0.12573673  0.11179118  1.059606e-01  0.14634309  0.13320560  0.10643279  0.10948257  0.12483287  0.14500055  0.12996698
KEGG_HISTIDINE_METABOLISM                       -0.030831971 -0.026347382 -0.05246956 -0.03817025 -0.03711451 -0.05239151 -0.02992710 -0.04339704 -0.04535416 -0.02246956 -0.068943683 -0.05028602 -0.063113563 -0.02707367 -0.05323869 -0.063275978 -0.03173868 -0.039525683 -0.02755053 -0.04591086 -0.06760272 -0.03666616 -0.02528646 -0.040320656 -0.044784334 -0.057674857 -0.06783511 -0.02118087 -4.757559e-02 -0.03079779 -0.03306480 -0.03762207 -0.04374289 -0.03096278 -0.01254511 -0.03899109
KEGG_TYROSINE_METABOLISM                         0.017578905  0.013796202  0.01327581  0.04762972  0.01224515  0.03037335  0.04467113  0.03453989  0.01369270  0.03704134  0.022735388  0.02729295  0.010396257  0.04953794  0.03065282  0.024393238  0.04694918  0.040233938  0.01044212  0.02743798  0.03891701  0.04757522  0.02613133  0.039036101 -0.011637129  0.007204219  0.04176325  0.02171444  5.394063e-02  0.02825620  0.04740187  0.02656193  0.05525311  0.01901562  0.06130051  0.03639278
KEGG_PHENYLALANINE_METABOLISM                    0.039387037  0.029253986  0.02751646  0.04138092  0.02542332  0.04090945  0.02613385  0.04694566  0.04409473  0.02669409  0.009505697  0.01810860  0.029763207  0.06543376  0.04989771  0.029176209  0.03209528  0.037862444  0.04544696  0.01254836  0.07318278  0.05544060  0.05343313  0.038427201  0.007101842  0.043387306  0.05281127  0.02894583  3.058806e-02  0.04347886  0.06369582  0.02896260  0.02467872  0.04490225  0.06313854  0.01977051
KEGG_TRYPTOPHAN_METABOLISM                       0.123296794  0.123012202  0.07613129  0.11525403  0.10856497  0.10334620  0.12704283  0.12708541  0.09159597  0.10202432  0.117859010  0.11469963  0.107325317  0.13152508  0.10459837  0.095553577  0.11230030  0.119066458  0.11008815  0.09174693  0.07821333  0.11181722  0.12158703  0.101828953  0.089254784  0.080564906  0.11224215  0.15882861  9.554444e-02  0.11310320  0.12619907  0.13651820  0.12255016  0.10789454  0.12458913  0.11276116
> 
> gbmPar <- ssgseaParam(gbm_eset, brainTxDbSets)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
                    TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up               -0.04270256          -0.1050256          0.12398917         -0.19785894          -0.0706204         -0.08331645         -0.04587976         -0.02691259           0.1493980          0.07636271           0.1292104         -0.02880156         -0.10622416          0.08485902         -0.02108542         -0.10255611         -0.04955077         -0.06055262          -0.1843912        -0.002264514        -0.000616764         -0.08413483          -0.1282847          0.10064219          0.16233229         -0.08391388         0.129510723         0.006051755          -0.0957773          0.05930173          0.07585551         0.122092770         -0.01523058         -0.17022164         -0.02753735         -0.09626334         -0.16239668          -0.1442122         -0.08378182         0.086702046         -0.06829592         -0.01859185         -0.10794134         -0.04824622         -0.02360036         -0.07829131          0.02113254          0.12831408         -0.05187672         0.021500630
astroglia_up                -0.24889633          -0.3181389         -0.16250310         -0.34518377          -0.2328486         -0.19025164         -0.20798167         -0.18978759           0.1634546         -0.18567656          -0.1220784         -0.14188750         -0.08219957         -0.18716765          0.08621605         -0.05093007         -0.23268801         -0.28527541          -0.2431186         0.280782610         0.051930564         -0.28603563          -0.2787882         -0.23358730          0.02706818         -0.17339069         0.007161405        -0.128829863          -0.2530055         -0.17991022          0.04954921         0.086976084         -0.19119326         -0.02761475         -0.10601965         -0.21094338         -0.17424458          -0.1764272         -0.25829321         0.183158653         -0.15279730         -0.15292932         -0.25484151          0.12260719         -0.09708606         -0.02624126         -0.03188327         -0.01503725         -0.17238517        -0.105109149
neuronal_up                  0.41365516           0.1370905          0.02258175          0.04140498           0.3739370          0.02504198         -0.09469289          0.21037816           0.2898127          0.02594733           0.4223345         -0.22630258         -0.21649319         -0.12661321          0.05458802         -0.15745561          0.22021627         -0.22540274          -0.1018101         0.108388420         0.248267146          0.15400529           0.2284369         -0.03153927         -0.06967695          0.04263526         0.379513854        -0.157687296          -0.1220727         -0.04305240          0.07266218        -0.007533977          0.14634095          0.25658376          0.45865011         -0.07414341          0.08676525           0.2972831          0.20881219         0.005408232          0.28084413         -0.11613621          0.17679797          0.32776928          0.01952200         -0.12391902         -0.24619662          0.49886083         -0.02607648        -0.001236969
oligodendrocytic_up          0.23276809           0.1579273          0.27834655          0.16541114           0.2967757          0.20073958          0.05308861          0.16548555           0.2960602         -0.06212319           0.2511061          0.23363850          0.49638543          0.20198656          0.02902960          0.30191162         -0.09088903          0.17653174           0.2923147         0.173427872         0.233041698          0.12377225           0.2739099          0.17169148          0.36533533          0.30762144         0.395886181         0.210670157           0.3295785          0.20726009          0.20552805         0.352208428          0.23866032          0.36220935          0.33072346          0.38151672          0.10382195           0.2867132          0.40519888         0.104315543          0.27453019          0.08890069          0.02961855          0.35470642          0.42481129          0.14658324          0.13577067          0.21517457          0.09820911         0.073203757
                    TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up               -0.12781345         -0.10424801        -0.003896955          0.23387421          0.25246844           0.3207035           0.1864102           0.2276360         0.264613462          0.16772316           0.1921236         0.150618790           0.2158142        1.480129e-01           0.2547912           0.2467531          0.16111355          0.19983249          0.07535168          0.28372256          0.14028380          0.14573966         -0.04131919          0.09047686           0.1447905          0.10384463         0.174769701          0.15962850          0.23867927         0.147562489          0.17203901          0.32877500          0.12467503           0.2831480          0.21697481           0.2582061         -0.04827454         0.070849773          0.10375364          0.05993822          0.14917783          0.03705593          0.28737667           0.1128391          0.15477895          0.16409778         0.143848674          0.08997557          0.25033466         0.200997387
astroglia_up                -0.33567021         -0.09558514        -0.267132320          0.27697125          0.04553025           0.1866003           0.1084145           0.1548024         0.115683387          0.08879166          -0.1794232         0.005649495          -0.1576545       -1.257789e-05           0.0727411           0.1555954         -0.05570396          0.07701213         -0.20774164         -0.04776384          0.13345907          0.02623989         -0.02663276         -0.05953059          -0.1011001          0.02571005         0.182406879          0.02375654          0.06349979         0.063565080         -0.03836509         -0.03293448         -0.03572666           0.1665919          0.16071904           0.2015802         -0.03462372         0.294133704          0.07912455         -0.09833367         -0.01426256          0.25177173          0.13323749           0.2085587          0.11625433          0.09270277         0.061118313         -0.01415236          0.09864426        -0.067173534
neuronal_up                  0.07027706         -0.02131532         0.238480842          0.38752317         -0.15659472           0.3577991           0.1892366           0.5672812         0.353841822          0.17010487           0.6047937         0.354282079           0.6087488        1.055863e-01           0.1732358           0.4886717         -0.06147035          0.24909699          0.54129393          0.09127180          0.05607375          0.28403989          0.41755055         -0.07975270           0.5899966          0.33505856         0.102693909          0.28051577          0.08310426        -0.006844963         -0.31495393          0.26595406         -0.30096794           0.4279460          0.10930434          -0.2523735         -0.27065562        -0.331425847         -0.04027485         -0.13510844         -0.02925798         -0.13647458         -0.06576075          -0.1651269         -0.23599409          0.08160665        -0.024158946         -0.39125116         -0.08528125         0.242973089
oligodendrocytic_up          0.26340390          0.20728662         0.238562146          0.03463889         -0.23287645           0.1609936           0.1784241           0.2769686        -0.005855304          0.17838346           0.2103914         0.079351508           0.1988334        1.691518e-01           0.1326108           0.2505812         -0.04892868         -0.03712413         -0.06713938          0.01717354          0.34941440          0.14144163         -0.01200277          0.09049891           0.2205388         -0.16470176         0.007669828         -0.08375967         -0.07398330        -0.023669180         -0.06730557          0.04221507         -0.02535599          -0.1434455          0.04683426           0.1519900         -0.01026107         0.006264224         -0.09514740         -0.09808242         -0.10883555         -0.08778694         -0.07144261          -0.1419069          0.01198113         -0.08184800        -0.006479715         -0.04310793          0.03696027        -0.009964341
                    TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up                0.23574567          0.27008722          0.11637555          0.16765565           0.1642266          0.03292988           0.2114207          0.13123819           0.2632937         0.255558714          0.12614825          0.22137032          0.16832484           0.2957996           0.2482320          0.20144142          0.29253731           0.3005284          -0.0101724          0.23305725          0.04509015         0.009178942        -0.001041475           0.2798335          0.03802142         0.055982875          0.10438785          0.05182689          0.10224425          0.05216468           0.0862304          0.02155929        -0.003172836          0.06739361          0.06256693          0.26367322          0.11536744          0.01256467         -0.01613898          0.09388852          0.11605589        -0.022074828          0.01870171           0.1159158          0.06165079           0.1766942          0.16406312           0.1409899           0.1558032           0.1268423
astroglia_up                 0.08497700          0.03829140          0.30608201          0.15711765          -0.1874617         -0.03283596           0.2290560          0.24698566           0.1847376         0.003580519          0.05081910         -0.04184080          0.23607570           0.1738209           0.1859548          0.11158631          0.02925080           0.2737893           0.3973568          0.25676961          0.39896998         0.362511205         0.397819214           0.3570748          0.25126109         0.160334429          0.40718110          0.34688248          0.36362766          0.26827732           0.3482736          0.31181324         0.269671812          0.31453886          0.29877113          0.44352730          0.40788910          0.14601178          0.31162191          0.29587323          0.37947936         0.349232664          0.33243016           0.2628245          0.34952493           0.2376603          0.14605626           0.3990569           0.3289481           0.2267814
neuronal_up                  0.28985543         -0.22610913         -0.06872989         -0.35634904           0.2051659         -0.15883492          -0.1861080         -0.17803520           0.1460343         0.105040208         -0.04944198         -0.33779090          0.29735931          -0.2133380          -0.3174639         -0.16643769         -0.20111679          -0.1413125          -0.1650908          0.01813617         -0.10455488        -0.296484567        -0.187537508           0.2442998         -0.07725316        -0.066574793          0.08146431         -0.06163985         -0.33529820         -0.25395066           0.2275310          0.48981934        -0.150285119         -0.09120100         -0.16014135         -0.01354999         -0.07519059          0.19440942         -0.18040416         -0.21007375         -0.10276626        -0.141371655         -0.21314137          -0.1962376         -0.14976707          -0.1246511         -0.17372631          -0.2207284          -0.1757595           0.1906853
oligodendrocytic_up         -0.04365214         -0.01038323         -0.06776547         -0.08472649          -0.1248816         -0.16991651          -0.1094051         -0.06642471          -0.2030105         0.013242268         -0.01680738         -0.03299205         -0.08840665          -0.2023591          -0.0859446         -0.06875004         -0.09073745           0.4037900          -0.0373881          0.12233991          0.07562161        -0.047601068         0.128217901           0.0132698         -0.15651784         0.007475202         -0.04953692         -0.13635011         -0.02535448         -0.07229950           0.1823742          0.37025576        -0.057417938         -0.06801955         -0.05093462          0.09347360          0.14824246          0.18023574          0.43900131          0.01998225         -0.04886937        -0.003561142          0.12171143           0.2173272          0.20198714          -0.2138286         -0.04280936          -0.1078011           0.2334409           0.1350531
                    TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up               -0.01384884           0.1922211           0.1338636          0.11847725           0.1641095         0.006294324        -0.008137892         -0.13724891           0.2054020          0.12997632          0.01119348          0.05979755           0.1010092          0.08196094          0.06026906        -0.000531532         -0.04216870          0.04782013          0.13415875           0.1741715         -0.04346128         -0.02707061           0.0641008
astroglia_up                 0.25182230           0.2092300           0.3504668          0.38080141           0.3572364         0.285424310         0.266573973          0.21241946           0.3210299          0.26738072          0.31228683          0.39524758           0.3530827          0.36410787          0.42455013         0.259007098          0.19900055          0.21611551          0.25564425           0.4072161          0.27182445          0.30879011           0.2296599
neuronal_up                 -0.21981790          -0.1745162          -0.1645862         -0.16331593          -0.1907196        -0.148526527        -0.150903069         -0.20298432          -0.1494018         -0.31979492         -0.07684811          0.12502843          -0.1325836          0.39917847         -0.26476090         0.306810092         -0.03434656          0.11584141         -0.25353924          -0.1629485         -0.11841551         -0.26324244          -0.1689706
oligodendrocytic_up          0.01801927           0.1762533          -0.1216974         -0.02033394          -0.1266508        -0.086965414         0.006808870         -0.05324112          -0.0283358         -0.08040521         -0.01867919          0.07793677           0.1875986         -0.10327650         -0.02771945         0.087825011         -0.13564146         -0.08870616         -0.02615045          -0.0209192         -0.07626177         -0.05744868           0.1065117
> 
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+                                 grep("_DN$", names(c2BroadSets)))]
> leukPar <- ssgseaParam(leukemia_eset, cgpC2BroadSets,
+                      minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
                                                  CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP                      -0.11212188        -0.09106815       -0.121150864        -0.08143375       -0.088090518        -0.07340947        -0.10376635        -0.12329046       -0.107490316      -0.1094321479        -0.09602253       -0.097841141       -0.052252012       -0.107114347        -0.10907601        -0.07366425        -0.12469120       -0.105311438        -0.11210642        -0.07831097       -0.095506069        -0.09272797       -0.080016602      -0.0601701101       -0.086388455       -0.086143328        -0.07964313        -0.07476053        -0.11573733       -0.106800817        -0.07058489       -0.083557328        -0.08462769       -0.090099523      -0.0549047537       -0.104821669        -0.12270687
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP                      0.12773870         0.11958013        0.169039831         0.08039046        0.079764086         0.04745847         0.17432542         0.10197508        0.108268340       0.2006370201         0.12760627        0.136610607        0.094614756        0.075754012         0.13272714         0.10349286         0.08997838        0.105152129         0.07972599         0.04842713        0.156201488         0.10861902        0.048660863       0.0486013305        0.094428151        0.067025764         0.07166594         0.02581748         0.01906544        0.053825100         0.11114079        0.146989381         0.08036877        0.070876416       0.1065750807        0.032006331         0.03126135
WINTER_HYPOXIA_UP                                         0.19660336         0.22220588        0.208150808         0.20369715        0.194220520         0.18637683         0.18791267         0.18394723        0.191934075       0.2073623135         0.18961007        0.206889571        0.227895816        0.218581670         0.19144735         0.22310948         0.19439608        0.202960622         0.20949776         0.19542339        0.216907511         0.24031950        0.208217532       0.2011029977        0.234533054        0.221475821         0.19919427         0.23800347         0.20715801        0.230102555         0.24544630        0.211888487         0.22075250        0.213354811       0.2209719414        0.212552165         0.19720964
PYEON_HPV_POSITIVE_TUMORS_UP                              0.12936217         0.08608186        0.156095439         0.04512521        0.100883198         0.11208812         0.12352973         0.17187068        0.153348975       0.1703012802         0.11051421        0.170675622        0.015252592        0.094679684         0.14160524         0.08032573         0.13750853        0.138672606         0.08985131         0.03661538        0.105799747         0.08113882        0.107166119       0.0506252281        0.047816290        0.095272447         0.10133515         0.08434566         0.11544536        0.046634453         0.06811758        0.136585794         0.09329885        0.066439827       0.0424873211        0.055346301         0.11044267
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP              0.10497861         0.11810250        0.130550079         0.08824334        0.067996562         0.09001761         0.10880848         0.09112328        0.114928671       0.1341928379         0.11162537        0.121156220        0.097889549        0.134823238         0.11398214         0.10943782         0.10538109        0.110901558         0.10004585         0.07652972        0.124448823         0.09605908        0.095401105       0.0800272992        0.125435027        0.107655114         0.07785774         0.11689738         0.10900193        0.126404590         0.13500916        0.118357443         0.12482627        0.132783820       0.0875660360        0.100749901         0.08896426
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP                 -0.14415962        -0.13112123       -0.148059446        -0.13794539       -0.137336129        -0.12385178        -0.12980927        -0.14141721       -0.145591804      -0.1413958552        -0.11800610       -0.144207294       -0.131972015       -0.141042585        -0.12498393        -0.14357730        -0.12949535       -0.154721081        -0.14240748        -0.12956549       -0.143591188        -0.13236731       -0.149298176      -0.1300145478       -0.131174376       -0.136769869        -0.12031729        -0.13417144        -0.14801656       -0.103740991        -0.11897875       -0.131464086        -0.12259302       -0.128755678      -0.1259053782       -0.135984581        -0.13075821
LU_TUMOR_VASCULATURE_UP                                  -0.08611663        -0.03840696       -0.075208780        -0.06571226       -0.059283399        -0.09743345        -0.01241906        -0.11715637       -0.095094587      -0.0942931758        -0.04907607       -0.091230456       -0.074117889       -0.052525843        -0.06551791        -0.04611678        -0.06288770       -0.095388286        -0.05466379        -0.02196421       -0.089002940        -0.02903084       -0.099934618      -0.0328273529       -0.059930837       -0.093726300        -0.06905892         0.03385055        -0.10159676        0.062777131        -0.04579346       -0.064021288        -0.02096713        0.041382070      -0.0659072134        0.004541717        -0.08085065
KORKOLA_EMBRYONAL_CARCINOMA_UP                            0.14802750         0.19989559        0.193531409         0.19043055        0.164415884         0.14670572         0.13835951         0.15782717        0.158620695       0.1923823767         0.17142120        0.191193516        0.189426831        0.200421860         0.17161690         0.21494495         0.18205192        0.192282258         0.16595727         0.17568860        0.212460788         0.19870684        0.195131434       0.1589439546        0.191376696        0.173976522         0.15799413         0.19036604         0.19127428        0.176196755         0.18543632        0.176852454         0.19522737        0.136840003       0.1714436876        0.171497790         0.18616571
KORKOLA_TERATOMA_UP                                       0.22823416         0.29024180        0.231155370         0.23171935        0.254748989         0.19408563         0.16835792         0.16188829        0.112118254       0.1565428797         0.20383020        0.123476972        0.217612011        0.244082034         0.22362179         0.28040203         0.20831738        0.168287700         0.24110595         0.23418356        0.244983055         0.25692773        0.200311939       0.2184469742        0.248702703        0.190689786         0.21178104         0.22717410         0.21281765        0.198438514         0.21014560        0.161257116         0.19694428        0.158841418       0.2076681127        0.196667083         0.21540144
KORKOLA_YOLK_SAC_TUMOR_UP                                 0.34466298         0.39892106        0.377886303         0.33108088        0.355059703         0.34014296         0.33424236         0.33551668        0.322514107       0.3587143377         0.35616777        0.345656031        0.361905734        0.356409761         0.34356338         0.36466181         0.35676080        0.353135417         0.34782607         0.35557146        0.369519925         0.37855110        0.340752613       0.3310743436        0.310692783        0.333271917         0.33092650         0.35381284         0.34636036        0.330627105         0.35041188        0.339198683         0.36176745        0.298834876       0.3344121129        0.355416500         0.34180114
KORKOLA_CHORIOCARCINOMA_UP                                0.44015614         0.48855227        0.450504964         0.46641488        0.448745786         0.41967427         0.40468719         0.44145971        0.455353414       0.5056625648         0.49198361        0.489745578        0.490534332        0.483410654         0.48684370         0.50623699         0.50398811        0.496025889         0.46027781         0.48204686        0.502594106         0.49342943        0.461528278       0.4453763188        0.453555580        0.457458981         0.44222231         0.48845097         0.47883248        0.485213780         0.48703015        0.459726900         0.46124201        0.434116406       0.4887206089        0.467923068         0.49059426
KORKOLA_SEMINOMA_UP                                       0.13847750         0.17850772        0.174597045         0.16508981        0.157223586         0.15596102         0.14187743         0.14411233        0.155857399       0.1758869779         0.17913681        0.168367099        0.161656280        0.177625715         0.15933775         0.16766991         0.17459358        0.187638049         0.16053712         0.18068610        0.160177064         0.16297719        0.143814313       0.1368714657        0.146708281        0.137036347         0.13672037         0.16405538         0.15687579        0.149515564         0.15499412        0.151293558         0.16531883        0.125764891       0.1551887231        0.172244543         0.16315928
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP         0.27744218         0.26350935        0.297888085         0.25976966        0.276608184         0.25693663         0.27761830         0.28848813        0.286664487       0.2762852086         0.27840239        0.291426599        0.282808179        0.294631962         0.29385340         0.26740892         0.28461746        0.296478631         0.29646299         0.26712951        0.297136943         0.29037251        0.290182379       0.2766321689        0.294832624        0.290120635         0.28546834         0.29985442         0.31836713        0.295872223         0.25619716        0.283982155         0.29792700        0.299964305       0.2675484590        0.301101215         0.29995819
HOLLMAN_APOPTOSIS_VIA_CD40_UP                             0.20838568         0.20620590        0.226021285         0.18903855        0.205996318         0.21204142         0.21967797         0.21308316        0.201127727       0.2021400473         0.20717155        0.215017814        0.187117852        0.219969815         0.21173231         0.19604622         0.21329915        0.212552604         0.19626079         0.19827681        0.211735913         0.19112536        0.203069987       0.2197126547        0.197947624        0.204388551         0.19946042         0.20608121         0.21291368        0.212708378         0.19862400        0.209122222         0.19925121        0.211899137       0.1938569725        0.222442050         0.21241407
LIU_PROSTATE_CANCER_UP                                    0.12333806         0.12822475        0.122836081         0.12725808        0.140594244         0.12825347         0.11034224         0.11649062        0.120184024       0.1301693730         0.12229130        0.129704667        0.137069254        0.111577549         0.11871748         0.11882426         0.12222041        0.139520829         0.11722272         0.12381120        0.128360065         0.13208683        0.142162149       0.1356536483        0.114693190        0.133318936         0.13748781         0.12832984         0.11667838        0.122081679         0.13437113        0.135333521         0.14198109        0.117064049       0.1415429031        0.128631348         0.11727950
LIU_SOX4_TARGETS_UP                                       0.08191204         0.05214134        0.096757396         0.07523797        0.079421912         0.07708861         0.08083627         0.10566201        0.079132766       0.0800895023         0.09502955        0.065630075        0.033165065        0.070986201         0.10605029         0.08258342         0.08768873        0.071996983         0.11390213         0.09018520        0.065872711         0.02685959        0.066144677       0.0727056296        0.082403808        0.073595763         0.06589577         0.06643292         0.09747230        0.106162263         0.04897972        0.066492306         0.06313290        0.112840981       0.0424372639        0.065643621         0.10517315
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP             0.12962537         0.11610080        0.145466087         0.12133965        0.151001465         0.12542172         0.12193757         0.11684710        0.124876198       0.1227735670         0.12962045        0.133337998        0.145216907        0.141828051         0.15001820         0.13815100         0.13460255        0.151878290         0.13727416         0.15746327        0.139912030         0.13476324        0.129655986       0.1284177003        0.132525587        0.130459851         0.12869022         0.13923393         0.13259415        0.155502893         0.13899383        0.126465783         0.14275177        0.146336368       0.1220863251        0.171552323         0.12417440
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP                 -0.04699784        -0.03856334       -0.028301448        -0.03891271       -0.045089149        -0.03704312        -0.02630941        -0.02816459       -0.029559739      -0.0534978383        -0.01366122       -0.041830107       -0.050639545       -0.040411674        -0.02102565        -0.03970615        -0.01799213       -0.033341689        -0.01897268        -0.01365414       -0.028107224        -0.02713442       -0.046683538      -0.0206629560       -0.018977519       -0.038659175        -0.03223894        -0.01494866        -0.02004138        0.028290459        -0.02212699       -0.038100635        -0.02119184        0.003239358      -0.0369081395        0.014342415        -0.01112552
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP                 -0.09394028        -0.10883789       -0.125696986        -0.07648813       -0.114219799        -0.09129576        -0.10820034        -0.09787250       -0.092631165      -0.0637997483        -0.07766220       -0.094268793       -0.082937625       -0.106384923        -0.08192685        -0.10758882        -0.08542658       -0.092203040        -0.06488157        -0.09003358       -0.111067169        -0.08970828       -0.114620536      -0.0850125408       -0.059028109       -0.122409700        -0.11287838        -0.08916244        -0.09472273       -0.077911670        -0.09390619       -0.097644568        -0.11001932       -0.078106059      -0.0940344476       -0.091955745        -0.07766899
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP                      0.02510931         0.08834848        0.080971697         0.01114658        0.025264412         0.04515388         0.06017182         0.06139166       -0.001637575       0.0902450722         0.02735733       -0.004243082        0.008884452        0.024612352         0.02882780         0.04029161         0.10199346       -0.025891095         0.01797175         0.03194774        0.099164270         0.07272077        0.001372288       0.0386279383        0.018516022       -0.003201053         0.04261062         0.04512323         0.05409370        0.082268487        -0.01156691        0.038932474         0.05063402        0.046801355       0.0762341100        0.031483923         0.09146968
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP                      -0.01159980         0.01773789        0.002741870         0.01471238       -0.003972485         0.01295277         0.02605081         0.02748918        0.012317275       0.0001521724         0.01504880        0.002445162        0.026606924        0.001673537         0.04936615        -0.01373036         0.01157459       -0.001213928         0.02950728         0.02709116       -0.001369139         0.01070392       -0.008326614       0.0005865785       -0.006947417        0.003683486         0.01476815         0.00833425        -0.02602648        0.005669794         0.02372157       -0.002592865        -0.01080445        0.018411711      -0.0002326556       -0.019837822        -0.02111218
FRASOR_TAMOXIFEN_RESPONSE_UP                              0.06343555         0.06524186        0.076096149         0.08623646        0.035901095         0.05553414         0.04813651         0.05000595        0.018630799       0.0361654200         0.04294741        0.045994056        0.084165291        0.039521918         0.04147761         0.03215540         0.04010818        0.043314016         0.07676386         0.04559031        0.070087913         0.07091543        0.059398083       0.0706534110        0.071532990        0.068066629         0.06426931         0.07338332         0.08518933        0.065149663         0.07183749        0.066367920         0.06594029        0.077125008       0.0927989288        0.074142612         0.07559066
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP                     0.03004809         0.05432805        0.001432391         0.02459771        0.011252625         0.04038848         0.02972862         0.01314790        0.002092703      -0.0156113936         0.04748579       -0.011117702        0.009640799        0.033918561         0.03840938         0.04608757         0.01172223       -0.005214653         0.03919416         0.04798752       -0.003693506         0.02843361        0.014212574       0.0239450749        0.022041404        0.002291239         0.03366971         0.04054535         0.02752102        0.053112241         0.05954476        0.008942285         0.01327435        0.032914846       0.0378134578        0.024061336         0.01399793
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP                     -0.03953071        -0.05465739       -0.007602480        -0.09969782       -0.064649394        -0.07536982        -0.04164320        -0.05312600       -0.043319892      -0.0119909722        -0.05473042       -0.040898014       -0.087901954       -0.049785859        -0.01812754        -0.08046669        -0.04513855       -0.042191116        -0.06131214        -0.08200335       -0.042998833        -0.05742151       -0.078783092      -0.1056325522       -0.069303843       -0.057059264        -0.07539755        -0.06329446        -0.06679513       -0.049903218        -0.05732776       -0.036949074        -0.04247288       -0.046862641      -0.1023930938       -0.071387634        -0.08894461
WATANABE_COLON_CANCER_MSI_VS_MSS_UP                       0.04819844         0.08558284        0.055708783         0.10324646        0.050709634         0.04995449         0.04822270         0.03763487        0.066913831       0.0260843037         0.03852020        0.041160906        0.092662161        0.050620558         0.03429650         0.05177460         0.08589703        0.046940975         0.04818196         0.04030422        0.077704576         0.10913606        0.057248585       0.0744440801        0.078206610        0.092934179         0.05650890         0.06626172         0.06222949        0.035216390         0.08404366        0.042016648         0.04474503        0.077050552       0.0877448713        0.057929757         0.02811160
> 

GSVA.Rcheck/tests/test_zscore_newapi.Rout


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> 
> ## 2023-11-10  axel: simple test script for method z-scores, new API
> 
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db


> library(GSVA)
> 
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
> 
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
> 
> p <- 10000 ## number of genes
> n <- 30    ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+             dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
           s1         s2          s3         s4          s5
g1  1.4171739 -1.3444519 -0.99052898  0.4203395  1.30716224
g2 -0.7281951  0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754  0.09779699 -0.6792548 -0.09124045
g4  1.0735382  1.3156255  0.15588330 -1.8079608  0.48531108
g5  0.7229884 -0.9162342  1.93982245  0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+                    paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> zscorePar <- zscoreParam(X, gs)
> zscore.es <- gsva(zscorePar, verbose=FALSE)
> dim(zscore.es)
[1] 100  30
> zscore.es[seq.int(min(nRowsToPrint, nrow(zscore.es))),]
               s1          s2          s3          s4          s5         s6          s7          s8          s9         s10         s11          s12        s13         s14        s15          s16         s17         s18           s19        s20         s21         s22         s23         s24         s25         s26         s27          s28         s29          s30
gs1  -0.397989121  0.63767552 -0.71152962  0.95681431 -0.39154705 -1.0418650  0.76943162 -0.22652269 -0.03794476  1.23795689  0.54741085  0.541307906 -1.3025217 -0.07350935  0.5617042 -0.110558260 -1.48434203  0.48341124  1.4582348818 -0.6596565  0.42366570 -1.18733982 -1.38666349  1.77213207  0.49521884 -0.54625805 -0.46923643 -0.326809131  2.03448230 -1.565153279
gs2  -0.292150055  1.00652251  0.59082177  0.60360826  0.09399124  0.3990216  1.16059005 -0.51857868  1.57864006 -1.82507931  0.27951753  0.015075493  0.7420740 -0.26993044 -0.1951051 -1.228360534 -0.29127936 -0.38907836  1.7217817461  0.4289776 -1.05871842 -1.92619800  0.16799779  0.27006041 -0.01617003  0.22027905  1.62510577 -0.140877183 -1.58374028 -1.168799069
gs3   0.286561399 -1.05214008  0.44954052  0.05225134 -0.27816203  0.5745265 -0.08816684  0.55254769 -1.29875323  1.56194900 -0.05237899  0.263111063  0.9526169 -1.98894869  1.9629224 -0.260586823  0.03510070  0.11049165 -1.0053564642 -0.7887344 -2.62545010  0.37942785 -0.80210329  0.63432226  1.52546755  0.14200823 -0.95287090  1.269227032 -0.32940645  0.770986212
gs4  -0.354767925  0.21855737 -0.54770518  0.57023369 -0.40119719  1.1654367 -0.85027787  0.05797497 -0.57666632 -0.19441172 -0.84753296 -0.201717192 -0.4443591  0.31037957  1.4397151  0.144981987  1.28913756 -0.76109926 -0.8188041253 -1.1193965 -0.34735329  0.02731708  0.47050049  0.36107874 -0.24978630  0.69621376 -0.34730205  0.335664905 -0.50390439  1.479089488
gs5   1.053567012 -0.90096227 -1.22439233  1.38286556  0.72832395  0.2446611  0.64214154  1.67034063  0.94014544 -0.56337436  0.13297430 -0.003270595 -0.4892865  1.04965180 -0.9017189 -1.422587378  0.25687151  0.34246303 -1.3100855881 -0.4117660 -0.56998370 -1.04747710 -0.59951317  0.38286581 -0.42463836  0.29869964  0.69420619 -0.224502898  0.01378260  0.259999076
gs6  -2.244409734  0.99135128 -1.25755227 -0.48107465  0.77088243  1.1587775  0.84165607  0.70800821  0.04455796  1.20866884 -0.08722013 -0.339734762 -0.3068380 -1.26475846  0.1691293 -0.016173483  0.08935879  1.04034445 -0.7302067427  0.3619944  0.09955336 -1.47161635  1.46668998 -0.57430525 -0.57827541  1.08697889 -0.36812846 -0.225673601 -0.63259981  0.540615686
gs7   0.052740026  1.67321048  1.06844511 -0.63335768 -1.29665110 -0.1715307 -1.66933194 -1.66163147  0.96745704 -1.98236849  0.39924531  0.780997272  1.5031445  0.82365265  0.7355819 -1.291690222  0.59198917  0.44201538  0.7748958150 -0.8715253 -0.42109173  0.38678646  0.62509742 -0.34088470 -0.73371942  0.45694938 -0.16347393  0.245014602  0.54802183 -0.837987628
gs8   0.128940466 -0.29023472  0.89066527 -0.61440040 -0.38274282  0.3546077  0.27907069  0.36742752 -0.96538900 -0.68424061  0.41316821  0.891427943  0.8562297 -0.82606670  0.9954917  1.271105299 -1.57441049  0.58613131  0.9237786732 -0.5526007 -1.00447106 -1.18216783  0.80591481  0.04182974  1.50238637 -2.48809418  0.67198869  0.329970369 -0.23288683 -0.512429049
gs9  -0.529924217 -0.50455633  0.14056762  0.82608534 -1.08452996 -2.4214825 -0.82702123 -1.51917889 -0.46117537  0.51536039  0.59351509 -0.477518222 -0.9141765 -0.36202472  0.2121035 -0.573687565  1.07691896  1.45448291  0.9987170368 -0.3781715  0.53631214 -0.44654865  1.24408983  0.30795693 -0.37080302  1.21990637 -0.38428269 -0.709115714  2.34614281  0.492038227
gs10  0.818321331 -1.51317539 -0.69457073 -0.49203352  0.36057893 -0.2397877  1.75081101 -0.06994105 -0.63367045  1.19094149 -0.90730458  0.767877575 -0.7928538 -0.06625141  1.5861559  0.979933067 -0.44783025  1.27989685 -0.4868701103 -1.0117896  0.94361547  1.85673623 -1.61731898  1.21625436 -0.28647246 -2.18059795  0.27744213 -1.003408010  0.30192017 -0.886608508
gs11  0.367678555  0.91252056 -0.42227266 -0.97087272  1.79158580  1.2585482  0.94342732  0.33332996  0.25752326  1.08956985  0.42462020 -0.463361537 -1.0340709 -0.62851508 -1.0342834 -1.514469249 -1.59087446 -0.08592467  0.5711694824 -0.2126554 -0.78142230 -0.16484959 -0.11708371 -0.06365675 -0.30699322 -1.78437695 -0.38348966  2.096264437  1.38197003  0.130964576
gs12  0.407633162  0.06089458 -0.03551973 -0.80557241  0.28472856  0.3839476  0.03138942  0.13026214  1.25696925  0.64914081  1.03413817 -2.014871071 -0.6371566 -1.64623803 -0.4174678 -1.889613999  0.17910813  0.02329786 -0.0009531196  1.3544298  0.64070445 -0.12299599  0.34538224 -0.04683912  0.06609172 -0.03387139  1.19121339  0.002288050 -0.67084599  0.280325902
gs13  1.117333034  1.17636696  0.90610556 -0.20339948 -1.76940395  0.6695672  1.67072725 -0.88508357  0.21042968  1.10554677 -1.20938609 -0.936796828 -0.5420542 -1.95749072 -0.1021446 -0.326335251 -1.38725541  0.03867057  1.2922253522 -0.2178358  1.11848269  0.61807105 -0.58824635  0.51758303  1.16189807 -0.11542606  0.56125057 -1.102475834  0.07801156 -0.898935092
gs14 -0.087991419 -1.48961560 -1.81093995  1.52077150  0.42263796 -0.2523003  1.81177614 -0.98653014 -0.44359835 -0.78718957 -0.27032118  0.208913565  1.4209980  1.20266088  1.0754392 -0.017917459 -0.55564302  0.04818988 -0.0639771402  0.5514408  0.12200747 -0.61335181 -2.18595402 -0.10832614  1.30303553 -0.18875480 -0.15271362 -0.366281115 -0.10674437  0.800279063
gs15  1.343950151  0.42076882  1.38439882 -0.88759686 -0.91178620 -0.4662795 -1.04143070  0.63814001  0.82957344 -0.29962403 -0.07941374  1.630590421 -0.5871337 -0.07434265 -1.5095501  1.553793983 -0.34571793 -0.82240473 -0.0947857521  0.8003060  0.21116056  0.32367880  0.86106297  1.65628788  0.97789380 -1.11080368 -1.05693195 -1.075624856 -2.14302463 -0.125154750
gs16 -2.280647404  1.45443048 -1.15615266  1.22715648 -0.91887150 -0.8774493  0.59718755 -0.53354106 -0.56650374 -0.69692215 -1.94787175 -0.263432001  1.8506749 -0.38045289  1.5196647 -0.171439192  0.23374260  0.12207975 -0.3457662199  0.8058231 -0.04857341  0.06274313  0.24285089 -0.52530011  0.36494819  0.51658411 -0.01130771 -0.356448130  1.77208671  0.310706625
gs17 -1.793915600 -0.76504524  0.63042343  0.52009464 -0.76953891 -0.6130846  2.30516686  0.87030325  1.22942353 -0.38676648  0.28786780 -1.294578572  1.0048342  0.34124188  0.6789841 -0.427903451 -0.26781132  0.36824855  0.1448156182  0.2312562 -1.65929393  1.39937404  0.85491251 -0.82632158 -1.70289841  0.74965589 -0.12891045 -0.156350687 -0.69636392 -0.127819267
gs18  1.076598555  0.66297942  0.31193924  1.21825571 -0.97634484  0.2376817  0.95228421 -0.69548369  0.64407889 -1.54705843  0.78530509 -1.141744986  1.0737459  0.20826231 -0.7801733  0.779895003  1.28313586 -0.72108935 -0.2461143875 -0.7458027 -0.38409736 -0.53680945  0.39463325  0.46243990 -0.97160166 -0.73933254  0.11490689 -0.850845941 -1.31226102  1.442617701
gs19 -0.932647493  0.36466764 -0.35976335 -0.48336730 -1.40727655 -1.7654296 -0.20079225  0.78943776  1.05075289  1.00527802 -0.38819134  0.067221765 -0.3143035 -0.09898034 -0.3791052  0.742819045  1.03125690 -0.29435736 -0.8584556405  1.5373474 -0.10243970 -0.45157605 -1.14712245 -0.58329174  0.09597807  0.98132256  0.98914383 -0.803965353  1.03267715  0.883162283
gs20 -2.507512451 -0.09179266  0.89256971  0.73127951  1.29936004  1.0227561  1.19748908 -1.12254621  0.39765236 -0.32497812  0.92840593  0.535525595 -0.6698568 -0.67309618 -2.7854267  1.470107881 -0.08598559  1.74783328  0.5261305573  0.1206040  0.50408329  0.08501165  0.83770748  0.10297851 -1.04236424 -1.27093846 -0.79581565 -0.156645031 -0.34413218 -0.528404617
gs21  1.590666101  1.21727966 -0.51796988 -0.70384659  0.47869886  0.6412920  1.08855268 -0.47402976  0.08376531  0.13287875 -0.58417864 -1.418465566  0.3586347 -0.06298446  1.0527743 -2.146897926 -0.23073419 -1.51825713 -0.0886423308 -0.8228190 -0.89776066 -0.01018669  0.03607537 -0.23848721 -0.91307940  2.16316601  0.88039149 -0.180082700  0.42559671  0.658650146
gs22 -1.314146576  0.56105707 -0.29581903  0.01879511  0.70153285 -0.4595619  0.79526977 -0.30610624 -1.59054925 -0.12272649  1.47363794 -0.919840374  0.3988845  0.50906124 -0.1078853  0.005275414 -0.80093636  0.02875750  0.1796627484  0.8606802 -0.14613823 -0.08254134  1.34492879  1.33240524 -0.72078684 -0.13081350 -1.79095355  1.829439862 -1.03960553 -0.210977661
gs23  0.007467771  0.87566015  0.10324376  0.43422509  0.89948175  1.4248760 -0.42838198 -0.63377944 -1.60531538 -0.81617333  0.71976579  0.178541229 -1.5026766  1.31351070  0.5908263  0.295870288  0.31272798  0.41614095  1.5239090790 -1.0149427  0.50905084  0.08055801 -2.05892070 -1.43447026  0.75255573  1.23995792 -0.53070949 -0.671543192 -0.97238791 -0.009068384
gs24  0.962632242  0.95541708 -0.19066384 -0.23175174 -0.76110030 -1.4063679 -0.89610030  0.66372973 -0.80965792  0.08779694  1.43555471 -0.290334626  0.2202661 -0.20314804 -1.7974438  1.986615879  0.30858557 -0.81071709 -2.1361827974  0.5564193  1.76375887 -1.03057351  1.32045107 -0.52316315  0.55080127  0.67747310 -0.41157504 -0.004477188 -0.66154101  0.675296303
gs25  0.750300473 -0.69054276  1.18919625  0.22555676 -0.89812453 -1.9043047 -0.08872006 -0.53073008 -0.25382802  0.61889062  0.54487413  0.150650635 -1.1560727  0.67452679 -0.4169377  0.301273856  0.27364471  2.12016724  0.2984327507 -0.7254619  1.57708274 -2.55299380  2.35308624  0.03326361 -1.15647532 -0.70205328  1.05030170  0.062511954  0.46103929 -1.608554943
> 
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+                     featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+                     sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+                                       grep("^REACTOME", names(c2BroadSets)),
+                                       grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- zscoreParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+                       minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
                                                    NA19099     NA18523     NA19144     NA19137    NA18861     NA19116     NA19130     NA19131    NA19119    NA19152     NA19153     NA19140     NA19138     NA18522     NA19192     NA19193     NA19239     NA19238     NA19210     NA19201     NA19172     NA18870     NA18858     NA18852     NA19159    NA18855    NA19204     NA18501     NA19127     NA19098     NA19093      NA18856    NA18912     NA18517     NA18502      NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                  0.08200762 -3.52041732 -3.26174022  0.51755585  4.3317957  0.20731183  0.79679064  0.79926124  0.8990293 -0.3162241  1.37146559  1.28865093  0.08780809 -0.04487147 -0.91082622 -2.01743735 -3.12498579 -2.43416998  1.66792540  0.63671241  0.98429879 -2.77176425 -2.57368171  1.08251788  1.86537795 -0.2611243  0.3413125 -0.86055908 -1.49156413  1.32126944  2.69602243  1.710794035  0.8409827 -1.34346099  1.04123139  0.362705265
KEGG_CITRATE_CYCLE_TCA_CYCLE                     0.22642469  2.71693263 -0.10717960 -2.55590909  1.8299224 -0.47957924 -0.54472874 -0.02445334  0.9176705 -2.7381498  2.48189970  0.83060592  0.38079534  3.38221199 -0.32877740 -2.83603934 -4.22277480  0.30241154  1.04250419  1.46120065 -2.03473559 -1.21891964  1.08436248  1.06426425 -1.55401694 -0.5226624 -1.2189195 -0.45981366 -1.44418236 -0.97635055  0.50837155  0.687584202  2.5479218  0.26221667  2.58838008 -1.048488516
KEGG_PENTOSE_PHOSPHATE_PATHWAY                   1.36770713 -2.36222774  0.04423311  0.12728501  4.5866555  0.73826068 -0.30430005  1.12280301  0.7386334 -0.4741849  1.94803182  0.77746818 -0.21649571  1.53618820 -1.14034304 -2.06467802 -3.35703927 -0.52856032  1.23074711 -0.38012652  1.09162981 -1.97458243 -1.97155134  0.40676902 -0.11013586 -0.8840621 -0.1723332 -0.55469059 -1.82128559 -0.27395469  0.21881375  1.100739928  0.2091012 -0.73264959  1.63276978  0.445364274
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS    0.24894806  1.15822465 -0.63403859 -2.85893527 -0.1383472 -0.23236162 -0.85909142  0.52113731  0.4042918 -1.2811704  1.65377601  1.05051126 -1.44312727  1.72029902  0.59548843 -1.29956124  0.13453374  1.14525277  1.29207698  0.58036810  0.53523531 -0.44979114 -0.57051676 -0.15789451 -0.25900848 -2.1421868  0.4292179  1.66346748 -0.71371117 -0.01810125  0.12724512 -0.774738588  0.2843053 -0.03222607  0.34212600 -0.021697443
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM             0.09155076 -1.97525177 -1.45276746 -0.07481523  3.5602457  0.21410187 -0.46891224  0.48276577  0.8301800  0.2782034  1.76137958 -0.30167366 -0.36866461  1.40519024 -0.46806431 -1.89929335 -2.77414056 -1.44200425  0.06351456  0.43244830  0.47487440 -0.05968271 -2.47979046  0.88521908  1.45849373  1.4370859  0.7227373 -2.42689891 -2.32001921 -0.69902703  1.80940353  1.445144270  1.1884455  0.36808537  0.73860677 -0.436670241
KEGG_GALACTOSE_METABOLISM                       -1.50220635 -2.12210786 -2.26086463  0.19222532  3.7806514 -0.02135668 -0.06191917  0.04740533  0.3036345  0.8632324  0.86542561  0.79337892  0.94383717  0.64846184 -1.52736862 -2.10108047 -2.57431539 -2.81169968  1.46044938  1.54579783  2.08963590 -1.37567056 -3.06980601  1.26834691  2.35203893 -1.1214375  2.0145262 -0.70745876 -3.08391089 -0.38893891  1.12194963  1.625915928 -0.1365118 -0.66174770  1.84065605  1.770831772
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM           1.62312696 -0.15873213  0.21618956  0.46858637  0.9166095 -1.04599221 -0.27045669  1.11594251 -0.7483182 -0.1238161 -0.08764850 -0.32826008  0.34447096  1.24438098  0.61296527  0.15432850  0.45526120 -0.36519590  0.20463352  0.04105416 -3.40788046 -0.10615080  0.03162673  0.30778305  0.76679284  0.7047822 -2.6927801 -0.49668598 -0.74070175 -0.19230287  0.78253260  0.019056184  1.1861060  0.56044201 -0.99809984  0.006350524
KEGG_FATTY_ACID_METABOLISM                       1.35637843  1.25200293  1.07298339 -1.71740038  2.3901222 -0.36157315 -0.61828083  2.30667544  1.7661146 -1.3820937  1.13392622  0.56871041 -0.79388010  1.09003603 -0.36094837 -2.90971040 -1.94439447 -0.01160654  1.33989630  0.15215352 -2.89938246  0.22556399 -0.77232732  0.57215286 -1.83412952 -0.7752354 -4.1289987  0.02530249 -0.63474809 -0.08583303  1.30223207  0.651511781  4.0322588  0.16603308  0.29172425 -0.465236301
KEGG_STEROID_BIOSYNTHESIS                        1.36553599 -0.12013577 -3.08293491 -1.34327805  1.3358376 -1.11364214  1.86689706  1.85283136  1.5670901 -1.7482283  0.54388973  0.03810215 -1.44328919  1.85735478  2.10172330 -2.62881691 -2.32801957  1.24532010 -1.02033468  0.69913015 -0.29822576 -1.97008651 -0.19118335  0.33269001  1.52165526 -2.1837464 -2.2547570 -1.83792686  0.06447423  2.18187799  0.88568269  1.120120992  1.0123686  1.94734636  0.53060126 -0.505924347
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS             -0.08350356  0.59893449 -0.18051314  1.46849025 -0.5398104 -0.94926659  1.14314746  0.90284639 -0.9560743 -1.7658533 -0.74679073  0.45581317 -0.76088516  0.75908154 -0.92291196 -0.68856752 -1.36785514  0.55938543 -1.85379029  0.65684292 -1.41481016  0.37705982  0.35137739  1.54211015 -0.08423593 -0.8595118 -1.1072458  1.75411782  0.91579317  1.05847124  1.52536833 -0.703220257  0.4891219  0.94531073 -0.02348034 -0.494945723
KEGG_STEROID_HORMONE_BIOSYNTHESIS                2.15700695  0.10244885 -1.53755271  0.84766905  0.5856113 -2.09650629  0.33261928  0.53843117 -0.6734007 -0.4685420  0.95573879 -0.82998047 -1.41476255  0.62639471 -0.09031677 -0.08950504  0.11011468 -0.44476912 -0.28512821  0.29866023 -1.98900643 -0.24411969 -1.43499147  0.86760041  1.02524276 -0.5932665  0.1374354  0.21201533  0.34436727 -0.41016807  2.07943956  0.425593065  0.3466719  1.06122025 -0.79768577  0.345420779
KEGG_OXIDATIVE_PHOSPHORYLATION                  -4.63240554  6.67049017  3.29453045 -5.55357439  0.5496431  1.77914583 -1.36568735 -0.24226839 -0.9307871 -1.1747541  4.67610019 -0.89434533  0.91778294  3.85769951 -0.94501694 -4.63557269 -3.61619441  2.54955115  3.68603811 -2.72776413 -3.86124115 -1.43398278 -0.68050376  3.04817148 -2.44714051  2.1306825 -0.6471011 -2.51904678 -2.43888735 -1.23953015  0.48985662  0.954496754  3.8663223  1.61356139  4.95225010 -3.050518657
KEGG_PURINE_METABOLISM                           0.62601378  0.18764292  1.73576348 -0.39598650  2.8634149  1.74410636  0.80345344  0.21606301 -1.3228291 -1.6357118  3.37382979  0.50309725 -1.50193862  2.70460008  0.64046292 -2.91457181 -3.24668292  1.31429488  1.82156620 -1.17862270  0.22910565 -1.92894788 -2.19958482  0.95864285 -1.79749826  0.3013226 -2.0561912 -0.90114440 -1.30231555 -0.50822552  1.03537654 -0.062022288  2.3525705  0.47295983  1.48590730 -2.417920862
KEGG_PYRIMIDINE_METABOLISM                       0.68740186  0.09101204  2.69635278 -0.42133976  0.8010248  1.80959049  0.21392008  1.07077719 -1.3103447 -1.9575492  3.30744108  1.47682356 -1.85296082  2.34519272  0.79412795 -2.39568143 -2.29502648  1.96378220  1.42298942 -0.45658368  0.59630261 -2.36440463 -0.67804226  0.66537108 -2.65018728  1.2139181 -2.3138877 -2.68945636 -1.24989873 -1.77690179  0.01581421  0.070503916  4.5215289  1.03102830  0.50944514 -2.892083563
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM  0.40749755 -0.34200633 -0.67837708 -1.23839426  0.6450508 -0.87406128  0.89718094  0.88623623 -0.5901204 -1.4540001 -0.87199772  0.42565207 -1.02900922  1.09092642  0.83055385  0.95392316 -1.75399991 -0.70209561  2.56557133  0.74972926 -1.57575278  0.32540715 -1.39589409  0.64504509  1.67331106 -0.4742681 -0.4768781  0.84809297 -0.83978189  0.95527769  1.45671942  0.108438034 -1.0078854  0.58026404 -0.78212513  0.041770444
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM     1.34480378 -3.30503462 -1.85282519  0.51114612  2.0581490 -0.56269049  1.33006959  0.04421460  1.1318004  0.3368706  0.50287384 -1.78230487 -0.50480571  0.94601805  1.04369734  1.71347618 -1.44995911 -2.43340216 -2.31170012  1.06556022  0.05794706  0.22204354 -0.97366673  0.37411217  1.72881970  0.3048721 -0.3882133 -1.42262378 -0.42158817  0.60165076  0.74800845  1.017367318 -1.4705719  0.31352222  1.51764940 -0.035286398
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM          3.05533939 -0.89909141  0.10954792  0.57235547  0.4626350  0.43289545  0.80738496  0.82828340  0.3856202 -1.2192401  1.88574795  0.99850668 -1.58048436  1.26624831  1.63212252 -0.17105083 -2.04406219 -0.17476728  1.10667030 -1.31693777  0.48580641 -1.58414785  0.05762645 -0.83033135 -0.25313737 -2.7494190 -3.0328378  1.09278033  0.12945747  0.94310449 -0.20656930 -0.008758587 -0.5489564  0.03192254  1.53794235 -1.202205950
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION   1.99685230  3.32822203  0.58345875 -4.52030235  0.3557779  1.04571821 -0.47089329  1.67689058  2.4018633 -4.7953730  4.07552302  0.75879243  0.62123432  1.51829109  0.78422115 -1.84905687 -1.97911844 -1.19127707  1.91957992  2.24311755 -2.31132941 -1.32123330 -1.89841999  0.56302584 -1.87052188 -2.8145421 -5.7964707  2.02162198  0.16550354  1.15166897  0.62682088 -0.514715091  2.6508192 -2.05463411  2.71049379  0.188390686
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS  1.21309346  1.03875454 -1.40361861 -2.52868933  0.4749534  0.80310065 -0.98833939 -0.71560160  0.3172929 -2.7148765  2.17790950  0.73901374  0.25849033  1.55020704  1.20997178 -0.08496525 -0.53778049 -0.39412463  0.91390937  1.51429190  0.98942311 -0.15970919 -0.70389239  0.07882245  0.51719734 -1.0064894 -0.3389961 -0.74168366 -1.24385664 -1.12735156  0.43249880 -1.443631927 -1.1247770  0.97292321  2.74297956 -0.686449461
KEGG_LYSINE_DEGRADATION                          1.27862971  0.71944399  1.63186710 -0.15625854  1.1239366  1.48957540 -0.71067310  1.03036572  1.0590009 -1.3259578  1.96846254  0.83164708  1.37283618 -0.32318559  0.82246557 -1.99572277 -1.13322958 -0.74814377  0.55359396  1.33240395 -0.03241343 -1.11966697 -0.40789253 -0.99695879 -0.31423848  0.5315305 -3.3596078  0.11542448 -1.01289512 -0.45023277 -0.42490054 -0.226806423  0.8458865 -1.67164998  0.99545026 -1.292086374
KEGG_ARGININE_AND_PROLINE_METABOLISM            -0.15234479  0.69098240 -0.76904212 -0.91208540  2.2065375 -1.38716533  1.98078525  0.27213689 -1.1158975 -0.9181385 -0.25718855 -1.95804902 -1.12474003  1.25322167  0.53928573 -0.73049153 -2.14409282 -2.25112459  1.25901808 -0.05875601 -0.95521014  0.40928361 -2.08064840  1.77638819  3.15870419  0.6818472 -0.8337812 -1.63164697 -0.97781157  1.68806097  1.53083443  1.557264638  0.1741774  1.04524198  0.46754689 -0.433102466
KEGG_HISTIDINE_METABOLISM                        2.68245243  1.47002186 -0.21440898 -0.53405078  2.0496709 -0.61763413 -0.26832178 -0.37983061 -0.5973106 -1.0657640 -0.90612550 -0.21298139 -1.00379460  0.17915007  0.94116346  0.18701698 -0.07179808  0.76376118  0.27104980 -0.74947548 -0.51319501  1.37082775 -0.09200211 -0.40229269  1.15117499 -1.9075314 -2.5648368  1.27744182 -1.25796002  1.29042314  0.68066731 -1.188354315  1.0593628  0.41174254  0.03668128 -1.274939998
KEGG_TYROSINE_METABOLISM                         1.91319390  0.74537191 -0.21049549 -1.42486425  0.5137825 -0.64566994  1.25615471 -0.66586315 -1.0869967 -0.7914632  0.10529750 -2.04374233 -1.41200636  2.03136776  2.15096014 -0.71526488 -0.41213522  1.77566582 -0.93917591 -1.12144350  1.31645784  0.85531594  0.03889139 -0.64170442  0.13590477 -1.9150054 -0.9753372  0.62223967 -0.54517272 -0.39983433  1.31049742 -1.405758842  0.7396993  2.28797364  0.70968153 -1.156521954
KEGG_PHENYLALANINE_METABOLISM                    1.71871162  0.85028780 -1.30449583  0.02082110  0.4768936 -1.66932255  1.68462411 -0.37651941 -2.3786373  0.7308768 -0.47484731 -1.97769588 -1.05075764  0.71056611  1.08003616 -0.61325382 -1.15603061  1.11546195  0.64651489  0.26703259  0.95952300 -0.67322170  1.09967677  0.27680080  1.06176322 -1.2410279 -0.2930592  0.65188967 -0.04065992 -0.62699333 -0.09001084 -0.001369905 -0.7343008  1.97832734  0.54187752 -1.169481219
KEGG_TRYPTOPHAN_METABOLISM                       1.16300387  1.44923733  0.64807218 -0.54150723  1.8798625 -1.75904518  0.40200001  1.19892690  0.7528380 -0.8030061 -0.00259142 -0.37058216 -0.79497393  1.00982067 -1.00764660 -1.04581411 -0.91849620 -0.59010610  1.71370618  0.38679017 -2.82420827 -0.14129154 -0.09195268 -0.23903564  0.93135542  0.4710853 -2.9961143  0.43059167 -1.18463698 -0.21792140  0.89276830  0.137376030  2.7846734  0.56166925 -0.53510897 -0.749738309
> pickrellPar <- zscoreParam(pickrellCountsArgonneCQNcommon_eset,
+                          canonicalC2BroadSets, minSize=5, maxSize=500)
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esrnaseq[seq.int(min(nRowsToPrint, nrow(esrnaseq))),])
                                                 NA19099    NA18523     NA19144     NA19137   NA18861    NA19116    NA19130   NA19131    NA19119   NA19152    NA19153     NA19140     NA19138  NA18522     NA19192   NA19193     NA19239    NA19238    NA19210     NA19201   NA19172    NA18870     NA18858    NA18852    NA19159   NA18855   NA19204    NA18501     NA19127    NA19098   NA19093    NA18856    NA18912    NA18517      NA18502     NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                 3.613776 -4.9679841 -0.49159131  1.17771731 2.7476858  0.9906586  7.8351036 2.3879352 -12.247507 5.1072799 -1.7088887  0.63969178 -0.43172043 4.310571 -1.08484087 -5.547877  1.76164051 -0.8898460  1.5516740  0.18384396  5.802682 -3.7757111 -0.84888911 -4.0044153 -2.8284060 -4.082546 3.4904554  -8.250833 -1.84490573 1.28570738 11.673596 -4.2948444 -3.9836382  5.0572394  0.389111698  1.27807521
KEGG_CITRATE_CYCLE_TCA_CYCLE                    3.477784 -4.3258387  0.10679683  1.15022124 2.7107418  2.7378566  6.9986362 2.9781870 -12.336655 3.6489484 -1.0391481 -0.52824121  0.65826573 2.792346  0.29220725 -6.488304  0.72250541 -1.4678365  1.2401595  0.68473909  6.985360 -3.7270434 -0.23551620 -4.2369070 -1.5168679 -3.622173 5.4307235  -7.795052 -2.44363904 0.63072187  6.965976 -3.1341445 -4.1118426  6.2243145  1.240638472 -0.66792044
KEGG_PENTOSE_PHOSPHATE_PATHWAY                  3.339370 -4.0330816  0.51583498  1.40649749 2.3302549  2.0374336  6.8119003 2.4065127 -10.353614 3.3243129 -1.0295482  1.11054456  0.15015971 3.222526 -0.22754631 -5.181391  1.31417726 -0.2722243  0.6939848 -0.36386838  4.818728 -3.5438041 -0.36599427 -3.3620882 -2.3822479 -2.812857 2.8927987  -6.781842 -1.39440389 0.65166045  6.613795 -3.4344536 -4.0261038  5.4529813  0.015849046  0.45574590
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS   1.344052 -2.2158240 -0.21175907 -0.53842579 0.7156543  1.5288896  2.5831229 0.9317288  -5.466600 2.2964636 -0.8651491 -0.50386448 -0.91065031 2.898462  0.03623637 -3.073694  0.20949331 -0.2369633  1.4088917  0.05340645  6.570503 -2.3938190 -1.06915911 -2.4866369 -1.0079189 -2.759769 1.9916084  -3.275961 -0.49396629 0.49476943  5.002457 -1.8388175 -1.2006148  2.8157552  0.127652664 -0.45955629
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM            2.631917 -3.4339405  0.76408579  1.94446913 0.3597460  2.0623149  5.8373764 2.2457127 -11.233068 4.4543105 -0.8609952 -0.10889232  0.29460916 2.556143  0.11638893 -4.873598  0.98963304 -0.2427547 -0.0727344  0.05007844  5.596166 -3.1119692 -0.66278612 -3.4164707 -2.3915290 -2.741625 3.6366017  -8.051503 -2.16851806 0.18545576  9.295116 -2.9409623 -4.3732252  6.2960637  0.230435983  1.13794800
KEGG_GALACTOSE_METABOLISM                       1.982906 -3.9655472  0.61138910  1.15467260 1.6497432  0.8209315  5.2419040 2.1089802  -9.470991 3.7134731 -0.5181230  0.27522867  0.47877266 2.465661  0.52640555 -4.480509  1.01519660 -1.0516291  0.7645887  0.11440946  4.035460 -2.7583348 -1.29899318 -3.1760242 -0.7767365 -1.936233 2.8326448  -6.897092 -1.60000462 0.14907466  8.487595 -3.6464832 -3.5973961  5.0170353  0.116352490  1.61167165
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM          2.062532 -1.7226116  0.04676367  0.09733945 1.3732660  0.6312735  3.1964202 1.1698729  -4.661225 3.5280417 -1.0282684 -0.24234280 -0.15789395 3.398797 -0.27367316 -2.285976  0.59113894  0.1038181  1.7998289 -0.70562100  1.466847 -1.9910010 -0.43593836 -1.5128138 -0.6582237 -2.253523 0.1210538  -2.828518 -1.52381952 0.63908058  3.312295 -0.9165812 -1.5677085  1.2962335  0.006141184 -0.07500485
KEGG_FATTY_ACID_METABOLISM                      3.386727 -4.2988297  0.06235647  0.58211164 3.3131963  3.0678691  7.0037479 3.2012797 -11.277464 4.2927549 -1.4335746 -0.45941305  0.29576869 5.354193  0.02688667 -5.924900  1.13628254 -1.0545026  0.3870266 -0.12197680  6.536312 -3.4052486 -0.74006237 -3.1208879 -3.6370863 -4.832566 2.5697139  -7.724517 -2.04579965 1.96532286  8.388591 -2.7458801 -4.0057123  4.2475503  0.401532299  0.60919695
KEGG_STEROID_BIOSYNTHESIS                       3.656540 -2.2721186 -1.57781964 -0.72604499 2.6915557  2.7253367  3.4859428 2.1396122  -7.766563 0.3563763 -1.7757330 -1.54337991  0.07930328 1.934096 -0.40859022 -3.366802 -0.91869676 -1.4728893  0.1800936 -0.22016331  4.432150 -2.6588099  0.96699753 -3.0431456  0.2835885 -1.981831 1.9816759  -5.436519 -1.29757797 0.75871060  6.245049 -1.8776229 -1.5097635  5.8384179  3.033017936 -0.93439173
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS             1.116348 -0.9463790 -0.45604407  1.85063315 0.8106916 -0.3276203  1.2722726 1.5051284  -3.911297 0.4279352 -1.1991834  0.27030319  0.37304589 1.394388 -0.30774860 -1.744298 -0.92604666 -0.4823653  0.6953440  0.31728853  3.213363 -1.1520835 -0.44496503 -0.7902377 -0.8179018 -1.481037 0.8903110  -2.713066  0.11460137 0.99717578  3.970424 -0.9784062 -1.0879326  0.8027559  0.375701324 -0.63109969
KEGG_STEROID_HORMONE_BIOSYNTHESIS               2.480574 -2.2365775 -0.76345941  1.00478856 0.6737178  0.9885282  1.2763885 1.3246518  -5.234984 2.4601178 -1.4631961 -0.46795704 -0.10691565 1.885405 -0.83051072 -1.461525 -0.76902369 -1.9770725  1.6275719 -0.31312275  3.542358 -1.2925407 -1.34198406 -1.8121874  0.4845320 -1.476588 1.6850644  -3.134337  0.07214458 0.57869417  5.589447 -0.1789734 -1.8021160  1.3544518  0.029050681 -0.39441569
KEGG_OXIDATIVE_PHOSPHORYLATION                  4.599553 -6.7100059  0.42751863  1.23309432 3.6403868  7.3503379 11.9441178 4.5820577 -22.111947 6.7108308 -2.6602605 -0.07351686  0.54111443 5.562369 -0.51723640 -6.354949 -0.32498263 -2.1480812  2.6116772  0.93083606 13.369164 -6.1648449 -1.26630351 -8.0783946 -5.1518001 -6.967977 5.0669407 -14.885391  1.28479521 1.01972315 14.812577 -5.0108056 -4.7390139 10.5574156 -1.074527837 -2.00447078
KEGG_PURINE_METABOLISM                          6.220789 -7.3332881  2.16396498  2.57568871 3.9859659  5.9240050 10.3558058 5.7052135 -22.077635 6.8238021 -3.0415523 -0.54372207 -1.11552134 6.029539 -0.46629110 -7.154343  0.67053421 -2.8913745  4.9291899  0.29117744 13.403968 -7.1225909 -2.44539633 -8.3994983 -2.7797096 -6.288009 7.2046295 -14.113059 -0.82453646 2.33187623 12.429260 -5.8244919 -6.9103465  9.8373238  0.195600901 -1.74696832
KEGG_PYRIMIDINE_METABOLISM                      6.251783 -7.3004492  2.45514238  3.55758788 3.5294787  6.1695147 10.5996032 5.4341495 -20.035750 6.8378927 -2.6453473 -0.25241143 -1.71619115 6.033213 -0.02466917 -7.150940  0.78178056 -2.2034922  2.5335758  0.25118554 10.327172 -6.6221964 -1.55381413 -7.3268938 -4.5723746 -5.782497 6.6734213 -12.451852 -0.73080869 2.09920973  9.852821 -4.1746574 -6.4184518 10.0207656 -1.585732321 -0.85976870
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 2.224928 -2.5175231  0.31954322 -0.05577043 3.0724152  2.4451896  2.5921602 2.1124348  -8.210483 2.8724531 -2.1070978 -1.60741186 -0.68246497 2.199909 -0.19364540 -3.650181 -0.42907746 -1.8261277  3.0553026  0.60745873  8.136535 -2.2790936 -1.58939303 -3.1084949 -1.7070042 -2.761089 3.4866388  -5.033765 -1.82076593 1.96304371  5.189870 -1.6042160 -2.6184510  2.5338460  1.312164296 -0.32183720
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM    2.999856 -3.4375039  0.89916682  0.63033836 2.4687629  1.9603347  1.1901481 1.6342611  -6.972969 3.0118818 -2.0881152 -0.72779749 -1.62320621 3.334605 -0.62335248 -2.686378 -0.91324037 -2.4721889  2.3887953  0.02658081  6.061305 -2.0460961 -1.20709007 -2.7982678  1.6860733 -2.621328 2.2711386  -5.897327 -1.23629767 3.63007666  3.537552 -2.4197078 -2.4758398  2.1078716  2.260659728  0.14729905
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM         4.528253 -4.1049604  0.95473848  2.35554742 2.7822856  2.4088547  4.0580919 3.0774039  -9.706246 4.2374134 -2.1616616 -1.01364410 -0.94299011 4.890240  0.03792379 -4.658464  0.24416843 -1.9253826  1.9851437 -0.79513338  5.959851 -3.1596842 -1.27828378 -4.1484755 -0.6797800 -3.179783 2.6697157  -6.646975 -1.44841945 2.43818842  4.976755 -2.7140771 -3.0367858  3.6516496  0.249454763  0.09506715
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION  3.578068 -5.2126760 -0.06582990  1.05028056 3.1175359  2.9255891  8.6648883 2.3315356 -13.262600 4.3087913 -0.4353979 -0.65613429  0.66965563 6.611628 -0.05894749 -6.337658  0.72653584 -0.9627796  1.2156060  0.23131911  7.440367 -4.5184377 -1.26578230 -3.5938565 -3.1877200 -4.678520 3.2011377  -8.745689 -2.57894300 1.66411861  9.113690 -3.2824421 -3.9956024  4.9755314  0.821735158  0.19100324
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 2.540325 -2.5580006 -1.05293097  0.95062670 2.7166826  2.4195780  2.5974731 1.1984907  -6.563815 1.1393911 -0.6535133 -0.53905503 -0.48018704 2.677603 -0.01257593 -2.979565 -0.07920138 -1.4780887  0.6527642  0.82805025  4.578221 -2.3827049 -1.46480651 -2.3355377 -0.5622099 -2.138416 3.8006165  -4.314880 -0.76030110 1.13881051  4.554075 -2.4839790 -2.0330791  2.0076049  0.891015248  0.18152038
KEGG_LYSINE_DEGRADATION                         3.602131 -5.1825796  2.10404410  1.03465213 2.2325113  3.8859631  6.2068738 3.2557411 -13.475952 4.4676256 -1.5475372 -0.64332512  0.30278276 3.096102  0.80316244 -4.861363 -0.16047923 -2.7961166  3.1711096  0.15946804  7.862459 -3.9302227 -0.46045256 -4.2726251 -0.8764999 -3.201900 3.8283383  -9.229505 -1.76236481 0.80665042  7.238060 -3.3994653 -5.0360166  5.6878045  1.220045863 -0.12912036
KEGG_ARGININE_AND_PROLINE_METABOLISM            3.552908 -2.6014549  0.25403717  0.44467074 2.9611366  2.7482330  5.2593925 2.8596838 -11.003736 4.4014280 -1.4301706 -1.48503133 -0.53070060 4.554944 -0.84220810 -4.833547  0.25503808 -1.8556128  2.1043602  0.08116681  7.166741 -2.6433864 -1.27027071 -3.8686066 -2.0615804 -3.311451 3.5978009  -7.755397 -2.32827010 2.16085780  7.856669 -2.3568083 -4.1579194  4.1342672  0.563638193 -0.62082177
KEGG_HISTIDINE_METABOLISM                       2.377756 -1.5661914  0.96968517  0.67672158 0.9721192  2.3359869  3.2557159 1.0090144  -7.185205 3.1549802 -1.8899941 -0.60468775 -1.07159899 2.157091 -0.57746861 -2.782320  0.04684621 -1.1830784  1.5261956  0.19975447  3.864136 -1.8653606  0.09025289 -2.5738520 -0.6662499 -2.626624 0.5408687  -4.116989 -0.76704574 0.94226265  5.226687 -1.5137978 -1.9567396  3.5069890  0.784552904 -0.69041273
KEGG_TYROSINE_METABOLISM                        1.678686 -2.8624559  0.11380858  0.96294524 0.6770510  2.7615384  3.4725219 2.3537463  -8.530014 3.5068974 -1.7874306 -0.61405904 -1.40109143 1.614691 -0.66315954 -2.873058  0.36251656 -0.9941132  1.1490792  0.76083067  7.367480 -2.0494605 -1.01357494 -2.6154799 -1.7935798 -2.941109 2.5428844  -5.886190  0.22349847 0.56447214  5.669252 -2.2344264 -1.0213345  3.1941475  0.652568301 -0.34807790
KEGG_PHENYLALANINE_METABOLISM                   2.090906 -0.6398089 -0.96814219  0.10793026 0.9964645  0.5346435  0.6255186 1.3708515  -4.156439 0.9251142 -1.8077444 -0.76133326 -1.10126175 0.105535 -0.33588778 -1.258697 -0.35343074 -0.9379906  2.7207387  0.00165670  6.070485 -0.5640568  0.14502636 -1.1017496 -0.7081219 -1.161937 1.3090258  -2.597788 -0.49159141 0.02963533  1.589456 -0.9849399 -0.2852917  2.7296313 -0.251299048 -0.88510761
KEGG_TRYPTOPHAN_METABOLISM                      2.427252 -1.8565270 -0.36746740  0.32340813 2.1446252  1.8352479  4.3807816 2.0802495  -8.862574 3.1187773 -1.1165949 -0.32613518 -0.01228540 3.252853 -0.62866265 -3.014655 -0.48220328 -1.8893938  2.7605496 -0.83247782  5.133392 -2.3976572 -0.27716429 -3.1951290 -0.5176048 -2.990382 1.8257622  -5.044709 -1.80260786 0.91193140  5.959211 -1.2696260 -2.5846251  3.4311657  0.932687520 -1.04941279
> 
> gbmPar <- zscoreParam(gbm_eset, brainTxDbSets)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
                    TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up               -0.08909934           -3.152221           0.8107079          -5.2069957           -1.033834           -3.508842          -3.1829696          -0.6973523            2.015886           1.1632330           0.8404895           -2.159491           -2.548436          -0.8250184          -3.4106404           -4.002532           -4.613817           -3.044947           -5.242683          -1.2277799          -2.5902555          -3.9951172           -5.281595          -0.1906933           1.3229285          -2.3332362           2.2376210           -1.582096           -3.701165          -1.7871696           0.1453581           1.3152286          -0.9330403           -3.939937           -3.847457           -2.256774          -3.6583197           -3.343534           -1.732189          -0.3798295           -3.595637          -2.2691422          -3.4280276          -0.6868929          -1.5292866          -3.6440129          -0.8287959           0.4759527          -3.1435814           0.6136584
astroglia_up                -3.10555037           -7.101899          -4.0708334          -9.6701263           -3.664210           -5.299715          -6.9344991          -2.4056788            2.838336          -4.0490130          -3.1252581           -3.831245           -2.365279          -7.0701428          -1.7311405           -3.642857           -9.353379           -6.868324           -6.498363           2.5117857          -1.8454742          -8.1922252           -8.284021          -8.5971607          -0.8126084          -2.3739610           0.8329655           -4.621603           -7.722374          -6.1625899           0.7790239           0.7748605          -2.9931959           -2.105014           -4.057559           -3.331656          -3.4418359           -4.645598           -3.835184           0.7608445           -4.037412          -3.3140937          -8.1346699           0.6228006          -1.9891070          -3.3462253          -1.0731883          -1.4644452          -5.1808878          -2.8928713
neuronal_up                  7.37537036            0.902553           0.3057596           0.2300378            6.512670           -1.073758          -3.5261610           3.0524882            3.747227           0.1086332           7.3042698           -5.441629           -4.460294          -4.1315377          -0.9454844           -3.971821            3.422017           -4.541850           -2.411690           0.8123934           1.3326064           1.2388876            1.226472          -1.2244988          -1.4490155           0.2784605           5.5226593           -3.202053           -3.079236          -2.3312546           0.4439339          -0.4968675           2.5700910            2.587650            4.151428           -1.103735           0.1977171            3.893207            1.635213          -0.4158050            2.809088          -2.6602840           3.1488241           3.7441383          -0.2328512          -3.6994980          -3.8924016           8.6663741          -1.6945566           0.3744679
oligodendrocytic_up          3.29318629            1.254525           3.2712757           2.7191887            5.272348            1.175787          -0.2208184           3.3361411            3.463337          -0.8905276           4.5060174            4.925995            9.254130           1.6478948          -2.4138339            2.381934           -4.283642            1.802069            2.652757           0.6540577           0.6721184          -0.2149802            2.097069           1.0987993           3.9911220           3.4783625           5.9792216            1.707458            5.240817           0.4118169           2.0783070           4.4474700           2.4108206            4.348025            1.816250            5.848493          -0.1675866            3.913055            6.890191          -0.1129943            2.247621           0.3634295          -0.8202027           3.2955322           5.6991646          -0.6973273           0.6332216           0.5563794          -0.7722805           2.2257859
                    TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up                -4.0501595         -3.58528280           -2.150553           2.6903341           4.4208691            8.164340           2.1478449            2.838322           2.5975997          0.37673200            2.838609            2.075690            3.310031           1.3772906           4.1679206            3.366810            1.771455           1.1231341          -0.3661421           4.8202400           1.8597821           0.2832633           -3.299052           0.4615451            2.080973          0.75936460            1.128923          1.91788210            3.565186           2.8923945            1.620005           3.9857385           2.1520939           1.5575374           1.4959032            4.756540           -2.867930          -0.6443480          0.85949798           -1.785971           -1.176208          -0.7720236            2.199689          -0.4467583         -0.06920086          -0.1063925          1.59512455           0.2113819            2.180979            1.594056
astroglia_up                 -7.8449103         -3.69159341           -5.755313           3.0432536          -0.4214884            3.141192           0.4343735            1.984018          -0.1593382          0.03139333           -5.837569           -1.925856           -5.373983          -0.4965235           0.8055162            1.604746           -1.688300          -0.5820614          -5.4221591          -1.9257791           1.7990137          -1.8344248           -5.126051          -2.2978494           -3.971752         -0.08022663            1.269094         -0.04203954            0.291440           1.2673922           -2.484940          -1.8906992          -0.3366926           0.1137957           1.2937214            3.049417           -1.620135           2.3199253         -0.15299389           -4.373301           -3.517849           0.7444723            1.008946           0.7440944         -1.30587497          -1.1595379         -0.12211222          -0.7345510           -1.016347           -2.525468
neuronal_up                   0.7621561         -1.58714007            3.908310           5.1544726          -2.8583933            6.461310           2.4198545           13.914963           4.5975953          1.16075755           26.315151            6.131003           28.314920           0.9021609           2.6534158           10.109527           -1.392535           2.0200464          12.5550187           1.4292865           0.5672497           2.9720049            5.488963          -1.8932872           22.021493          4.08113876            1.624494          4.29047134            1.231357           1.0326487           -6.201044           3.2394715          -4.5485246           3.5140611           0.8060133           -2.388428           -5.656942          -5.3246569         -0.02576302           -2.989774           -2.180673          -2.7829681           -1.709889          -4.0113452         -5.27955635           0.1081630         -0.65506207          -5.1568867           -2.899157            1.900477
oligodendrocytic_up           3.4473515          0.08207331            2.122737          -0.4139425          -3.6839021            1.784584           1.6375784            3.111439          -1.1400225          0.24599609            2.236097           -1.539376            1.530867           1.2539415           1.4258764            3.523489           -2.181047          -2.2383685          -1.0576358           0.2384092           4.2246382          -0.1492978           -3.327585          -0.7908182            2.860221         -1.23331168           -1.455083         -1.56496385           -2.848318          -0.4789735           -1.910726          -0.6964973          -0.9156850          -3.7150977          -0.1130542            3.021765           -1.968815          -0.8635538         -2.90146119           -3.962522           -4.266302          -1.8826848           -2.813841          -3.7335868         -2.67976967          -3.3860511         -0.08389153          -1.4103498           -1.328776           -1.187159
                    TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up                  2.676893          4.30587603          -0.1484128            2.121824            1.193762            0.216868            2.098520          -0.3590077           1.4924973           3.1318506           -1.885732            1.708314            2.657195            4.545553            2.912760           1.9804288            3.802850            4.534642        -0.003929236           3.2517485           -2.888534           0.1771372          -1.1738971           2.8936005           -2.743719           1.2918124          0.08247081           -1.203403           1.4767707           -0.304507           -2.321400          -0.4437532          -0.3035455           1.4292700           0.6915937           4.0222928          0.19722388          -4.5950920          -0.9341628           0.3305044           0.1631184          -2.8586504          -0.5955305          -0.2539437           0.8313484            1.589897          -0.7911376            1.293819            2.079665           0.9014619
astroglia_up                  -1.410315          0.04597652           2.5770285            2.311639           -3.398351           -1.272882            2.373027           1.6009710          -0.2377814          -0.0469951           -3.575104           -3.168532            2.258187            1.899525            1.815670           0.1310026           -0.363329            3.570761         8.762186646           3.2915183            6.806357           6.3444795           5.9779424           5.6455262            2.528754           3.0563019          8.59482813            2.857618           5.3890853            3.179268            3.523551           3.7860581           3.8898683           6.9126141           4.3234965           7.5338826          4.60504082          -0.2121851           4.2592086           3.3834519           4.3762196           5.9914008           5.4677275           2.1915212           6.4911546            2.848080          -0.7855700            4.469387            5.496258           2.8326382
neuronal_up                    2.935035         -4.33202655          -2.3779648           -4.899466            1.924114           -2.897353           -2.767796          -3.8811350          -0.3370994           1.1164572           -4.545340           -6.060301            4.539371           -3.571778           -5.669859          -2.6699004           -3.006828           -3.455450        -1.900261556           0.6429803           -3.745943          -4.3142406          -2.7433338           2.6788158           -2.270892          -1.1439441          1.03773052           -2.029232          -6.1026313           -3.833959            0.559603           8.2443008          -2.5442885          -0.3626451          -2.5297864          -0.5810968         -2.26408321           0.6219462          -2.1951042          -3.4844647          -2.0629756          -3.2574162          -4.6249237          -4.2837280          -2.9083139           -2.304073          -4.9578554           -3.231750           -2.616099           2.6652850
oligodendrocytic_up           -1.429602         -1.16836372          -3.3273872           -1.484285           -2.102452           -3.335235           -1.695018          -2.8550582          -5.1228981          -1.1518311           -4.754625           -2.497824           -1.200832           -3.091723           -2.826340          -2.3319305           -2.020322            5.901598        -1.869680552           1.5415212           -1.287606          -0.8869270           0.6441386          -0.9799234           -4.562924          -0.1648678         -2.00977500           -3.914152          -0.6328189           -1.448776           -1.641520           4.8529785          -1.1013767          -0.1757191          -1.5306714           0.6552283          0.05824521          -1.7220446           6.6503840          -0.2605514          -1.7376517          -0.6012265           1.1494110           0.9321423           3.3145489           -3.385071          -3.7834245           -2.604791            2.660582           1.3763185
                    TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up                -1.5182935            1.414137           0.6145721           1.3611626           0.9299387          -0.6118263          -1.9077298           -2.977643            2.354636            1.256214          -1.0446336         -0.03521543          -0.2048689          0.08255436          -0.5703374          -0.5160375           -4.393404         -0.04869947           1.0193142            1.716183           -3.050138           -2.968484          -1.4182898
astroglia_up                  3.6679577            2.016040           3.8365848           5.3857249           3.6519214           4.1911267           2.2371880            2.996960            3.653019            2.850722           5.3799630          4.07607902           4.5965300          3.82064210           6.8146847           2.5472498            2.787112          3.48964654           3.3631687            7.909505            4.609892            2.788675           1.2952133
neuronal_up                  -3.5923614           -2.462081          -3.0230934          -2.2989952          -2.9441875          -2.8335093          -2.8902359           -2.778339           -2.445036           -4.896693          -0.7803416          0.16600660          -2.5170378          4.64377108          -4.2430666           3.5077554           -2.229394          0.68892787          -4.1220154           -2.572970           -2.437011           -4.344700          -3.5499763
oligodendrocytic_up          -0.4309207            1.205395          -3.3004554          -0.2007412          -2.3954090          -2.6221966          -0.6024445           -1.075083           -2.183149           -1.983176          -0.3895268         -0.45898726           0.9638120         -1.89896706          -1.4509535          -0.1200174           -4.067190         -1.98215669          -0.5922569           -1.755122           -2.906155           -3.149109          -0.9366359
> 
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+                                 grep("_DN$", names(c2BroadSets)))]
> leukPar <- zscoreParam(leukemia_eset, cgpC2BroadSets,
+                      minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
                                                  CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP                       -2.3189547         0.55622710        -3.11198172          1.4986887         0.79561210         1.27047787        -0.65748275         -3.6475523       -0.938530423         -2.2124263        1.492202601        -0.73476415         1.14702413         -1.8556094        -0.10710987         0.62555189        -1.84985291        -1.99696364         -1.6391298          0.7733034        -0.76199840        -0.11481253        -1.54473797         2.90988107         1.91589932        0.306170802         1.84065500          1.0454556         -1.7550145        -0.64379309          3.1809700         1.66381825         0.85600132          1.5031001         5.27303344         -0.3741954         -2.3891628
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP                      -0.1437327         1.34145819         3.12030398         -0.9451609        -0.65236606        -0.75734866         2.49198413         -0.6960575        0.479216286          4.2298075        1.699907478         1.80608946        -0.55495287         -1.2596018         0.67756954        -0.22151006        -0.57450357         0.22116396         -1.9389978         -1.6951874         1.38964755        -0.02115285        -0.93820411        -0.54585990        -0.77666967        0.094771714        -0.46941562         -2.4584473         -3.2781747        -0.41248115          1.9550954         2.96291598         0.77692080         -1.1198979         1.01968846         -2.1157809         -2.6910370
WINTER_HYPOXIA_UP                                         -2.2032116         1.94192756        -1.01905531         -0.2262124        -1.70570515        -1.31370553        -1.53784382         -4.1896689       -0.573056157          1.3188203       -1.630985843         2.11056496         3.86978019          1.7943601        -3.47417711        -0.09511845        -1.03683603        -1.41318482         -2.0541609         -2.5022841         0.95884756         1.99489650         0.01912947        -0.40707157         1.49731005        1.876664626         0.82794692          1.3034511         -1.9570481         1.23100844          4.5355537         2.45428354         2.43716611         -2.4481408         1.95214281          0.4155076         -2.7518949
PYEON_HPV_POSITIVE_TUMORS_UP                               1.8425924        -0.90371747         4.42311845         -3.7133346         1.07235312         1.59420262         1.54184230          5.1765404        4.512483991          5.3940779        0.528141105         6.86588624        -5.27763956          0.5196579         2.48547689        -1.84517673         2.66475634         3.44169814         -0.7470868         -5.1281340        -0.05626604        -1.23659933         0.25586378        -3.15164039        -4.16550799        0.041309197         0.47627197         -2.3210603          0.1246063        -5.22630542         -2.5795122         3.27132937        -0.03055620         -2.0519735        -3.90153690         -3.1462161         -0.7499449
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP              -2.0355786         2.60368733         1.65952935         -0.2731903        -2.82481184        -1.60635471         0.40429957         -6.5356063        1.373085999          3.2217230       -0.004117969         3.12303563         1.37715940          4.3192977         0.04425356        -1.21708631        -2.06097063        -0.94940011         -2.9791103         -4.4507436         1.15163993        -2.13360896        -2.04857971        -2.73828950         3.09070632        0.890670934        -2.19450875          1.7569005         -2.1019689         1.35470426          5.2654387         2.89066529         3.53097016          2.9110126         0.45673634         -0.7116174         -4.5599727
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP                  -6.1743193         2.10626458        -9.93033191          5.5020838         1.24528029         2.76706915        -0.76977556        -10.1318343       -1.226965247         -0.2985038        3.204167870        -2.06583449         4.01539216         -1.4989300        -0.80243199        -2.09676668        -3.92339728        -4.76956131         -3.5492403          0.6307940        -6.10750595        -0.36445017        -5.33447764         3.97968003         1.06375876       -1.501968354         4.59460616          3.0050082         -5.2099545         4.59692879          8.4071865         3.02679350         4.62088574          4.2776647         8.40747357          2.6954767         -2.3902658
LU_TUMOR_VASCULATURE_UP                                   -2.3516037         0.23422156        -3.24709239          1.9002877         1.06371531        -0.31124003         0.64150436         -4.4921642       -0.429394270         -0.4708068        1.209418772        -0.53680406        -0.18120399          0.1020756        -1.17510637        -0.13495767        -1.60844266        -1.61180192         -0.2395109          1.6463378        -2.91072538         0.28004166        -1.85054840         3.12872425         0.81025980       -0.427636238         1.02779187          1.5058078         -3.8168552         3.69953701          1.2982542         1.83497935         0.73751145          2.3115023         1.90714553          1.9502801         -1.4935021
KORKOLA_EMBRYONAL_CARCINOMA_UP                            -2.0102420         1.77944838         0.71764392          0.7225229        -0.47650814        -2.94754400        -1.68662524         -2.7193614       -0.282629306          0.8789733       -0.663623433         2.48363943         0.58547469          0.9084250        -1.30090891         0.91028023         0.22038861         1.58879655         -1.9871067         -1.0238739         2.48127825         1.11685683         0.80172070        -0.88055998        -1.02367666       -0.170070225        -0.56110595          0.9707670         -0.6937145        -0.51027108          1.3912644         1.21188680         1.78787521         -2.5882821         0.35238902          1.0686185         -0.4521463
KORKOLA_TERATOMA_UP                                       -0.3532193         2.17997348         0.03956106          1.3024658         1.85511030         0.23121185        -1.71392644         -2.2452103       -1.891420902         -1.2620777       -0.745760801        -1.54879367        -1.14580035         -0.4412586         0.13971105         1.04541604        -0.18902172        -0.56554466          0.0430148          0.3175348         1.08482965         0.62953613         0.19987932         1.49131527        -1.44961377        0.238083305         1.05678681          1.2490852         -0.7551186        -0.06277113          0.4286523         0.11269812         1.05268675         -1.7303152         0.59079381          1.2819498         -0.4704426
KORKOLA_YOLK_SAC_TUMOR_UP                                 -0.1040637         2.99594415         1.31530981         -0.3081178         0.62832670        -2.42448384        -1.00992574         -1.6262212        0.163843219          2.4035673        0.155357913         2.06606337         0.24037257          0.4130723        -1.10335321        -0.70220925         0.89210405         1.60172761         -1.0474659         -0.7906492         1.09211241         1.15544503        -0.36703662        -0.60395345        -2.57074459       -0.583146941        -0.73629462          0.3110249         -1.7065781        -1.25258365          0.9935598         0.79136836         1.51933857         -2.7892840        -0.09963966          1.6070600         -0.5198466
KORKOLA_CHORIOCARCINOMA_UP                                -0.3744594         1.47839993        -0.77812840         -0.2217174         0.83857394        -3.22690712        -1.70821076         -1.8247392       -1.096790972          0.7766130        0.106430602         1.53596539         1.48267931          0.3337191        -0.10364576         0.33957176         0.78113867         0.08030119         -1.7081769         -0.9363552         2.19093776         2.26944769         0.71838354        -0.24247756        -1.29633819        0.701466602         0.09347977          1.4125416         -1.8054660        -0.61006004          1.4158132         0.45544767         0.58758936         -3.0940532         1.23411751          0.5310415         -0.3361331
KORKOLA_SEMINOMA_UP                                       -2.9340089         0.09586312        -0.67073745          0.4686024         0.58281055        -1.86617285        -1.39432462         -3.8666739        1.166840265          1.9282066        0.806977219         2.90705383         0.99184039          0.1234681        -0.96569590        -1.16396240         0.28761478         2.57697201         -0.8848146          0.8255735         0.58071491        -0.18386443        -0.64027729        -0.33107070        -2.65069999       -0.739030827         0.26850943          0.6218152         -1.5319993        -1.03372781          1.5970938         1.42233007         2.14424171         -2.9444395         2.36223981          2.5275209         -0.4847880
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP         -0.1871021        -2.72933254         2.10389786         -1.5218035        -0.24851512        -1.94879594        -0.11225920          1.3387953        2.092476554         -0.5027557       -0.734496247         1.48332203        -2.06908392          2.1504269         1.57346111        -2.67286549         0.55601780         1.75728633          1.0591640         -3.5172751         0.41769901        -0.15799519         0.10733345        -1.26412040         0.62132681       -1.068445939        -0.81184190          1.7795510          2.8672636         0.51834308         -2.2301655        -1.72721639         1.30982203          0.7498270        -2.26434985          1.7641941          1.5182121
HOLLMAN_APOPTOSIS_VIA_CD40_UP                             -0.7820872        -2.13675642         3.39698951         -2.1548508         0.90823798         1.87534780         1.18216325         -0.3454263        0.519486282          0.7495966       -0.702832818         2.65768682        -1.39601416          2.9377153         0.01460505        -3.73008343        -0.30955544         2.04220857         -2.8652428         -3.1013878         0.38820637        -1.85976238         0.14583211         1.54497828        -0.51769728        0.030388041        -1.27655961         -0.1068228          0.1140717         0.19735404         -1.8393420         0.06094494         1.18064262          1.7171987        -0.09629675          2.0372182         -0.4801540
LIU_PROSTATE_CANCER_UP                                    -2.7418994         0.36658204        -3.31691584          1.3184501         2.30781570         0.78372138        -2.49394355         -5.4987675       -0.822790802         -1.2417137        0.174898665        -0.25341599         3.10520813         -3.4272596        -2.36564481        -1.46486084        -3.27025426         1.45149707         -1.9796783         -0.2385052        -0.10360642         0.41913964         1.31326282         2.25499078        -0.48834592        1.569427440         3.08573035          0.6747347         -2.1158608         0.88924255          2.5723039         2.39831139         3.32890627          0.5872895         3.74319390          1.1868815         -1.7081250
LIU_SOX4_TARGETS_UP                                       -0.3751389        -1.95588700        -0.83556096          2.8406515         2.03541886         1.67651015        -0.06264359          1.0278755       -0.621726452          0.1542651        2.093682904        -1.12917548        -2.22483713         -1.1771779         1.46468782        -0.49621654        -0.06320445        -1.49441905          1.4408110          1.3723181        -2.65175416        -5.32222009        -1.90422195         1.32712098         0.41560025       -0.141050306         0.65594298         -0.6743251          0.5105999         2.58778466         -1.0269048        -0.06555656        -0.16265033          2.7736846         0.23669453         -0.9452083          0.7162302
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP             -1.2464061        -2.52190564         0.34481699          0.6136117         4.14525942         1.31851001        -1.50928145         -3.5261653       -0.376143666         -2.1419889        0.263685045         0.03051013         2.23927375          0.2887824         0.30432686         1.08666353        -1.81678277         2.91665062         -0.4815280          3.7840202        -1.28255238        -0.92708160        -1.47494702         0.36348866        -1.35695710       -1.365236115        -0.09332459          0.6773143         -3.3005646         1.08982967          1.3469267        -0.15650030         1.18988291         -0.1304936        -0.41848104          5.7424208         -3.6196334
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP                  -3.8776379        -1.06789926        -7.00642158          5.2446555         1.06812916         1.14091106        -1.23350873         -7.0151593        0.787783143         -2.2876206        4.506629996        -0.82513916        -0.50395314         -2.3986535        -1.14874866        -3.70233709        -0.71755286        -1.99280231         -1.4519194          1.8781710        -5.50515340        -3.26577909        -6.14460283         3.77798602         1.26457017       -2.522562013         2.00592405          2.4181014         -3.8502790         6.01626665          3.2565317         1.33592939         2.78983801          6.8105203         5.47203316          7.8148200         -1.0710708
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP                  -0.5530494         0.91449001        -5.10684798          5.8892478         0.70327111         0.68010952        -1.35401240         -4.1731715        0.829970887          2.0186035        0.734848132        -0.53350919         3.00824815         -1.7128629        -2.31656387        -1.10739140        -1.78453464        -1.33346346         -0.1610865          0.1636164        -4.61596682        -0.04388835        -2.22820486         3.50293537         1.08838500       -0.856531524         1.18347365          0.7537940         -3.2931554        -0.12534415          2.1550084         1.22544443         0.02188584          3.0547016         4.00283815          0.7785386         -1.4098262
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP                      -1.0842740         1.15191033         0.19359086         -0.2177736        -2.01743872        -0.35397625        -0.86551082         -0.6587418       -1.482192451          0.5834861        0.095377824        -0.80250318        -0.03850151          0.1414836        -1.48102277         0.70702073         0.54101179        -1.89001468         -0.1428820         -0.2992931         0.06876902        -1.27262670        -0.73299530         0.15317029        -0.21894175       -0.995729217         0.31049138          1.3867304          0.8623611         2.09995277         -1.6338695         0.65923937         0.40301566          2.6698444         1.87944620          0.4256969          1.8556888
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP                       -0.6904303         1.93458550        -1.99458125          1.5799006        -0.04746809         1.35845690         1.35954571         -1.3239543        0.183594189         -0.7304046       -0.867718542        -0.16037922         1.01551852         -1.2458131         0.36381625        -0.77975659        -0.36807781        -0.37384028          0.5956824          1.1883224        -0.48945985        -0.09633758        -0.76459822         0.07532145        -0.07071889       -0.592753031         0.03215539          0.4208453         -1.3262166         0.06108885          1.8490292        -0.26820419        -0.03938847          1.1315785         2.00315374         -0.7778437         -2.1446504
FRASOR_TAMOXIFEN_RESPONSE_UP                               0.5413132         1.28746036         1.36441186          3.3368271        -1.31891545         1.57406315         0.31091232         -1.8851886       -1.508855984         -0.2751830       -0.859463551        -0.54855067         3.08124648         -2.9190068        -2.21050219        -1.68670629        -1.28382294        -0.29745413          0.4018516         -0.7913413        -2.31590360        -2.18097162        -0.89954411         1.44692469         0.04672709       -0.343429133         0.79945007          0.2049267         -0.4953848         0.11145147          0.2050700         0.26420024         0.55065832          1.2372609         3.15265775          1.3700061          0.5328047
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP                     -2.6864978         3.43756903        -8.37492717          3.4513206         0.39310486         2.00425397        -0.88377471         -6.5962386       -1.122346365         -3.3992922        1.699856481        -1.83778409         1.82943931         -1.0046215        -2.58511818         0.68047190        -2.39298391        -4.23623360         -0.4038435          3.2643617        -5.42149983        -0.47681907        -2.08912701         3.41957446         0.43726984       -2.000731185         4.26612070          1.7425539         -3.2522439         1.90242944          7.7104250         1.33084413         0.94700410          2.9575476         6.54983238          1.8646617         -1.1245584
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP                       0.7708646         1.64610911         2.90389826         -1.5098526         0.68514559        -0.62856125         1.44344048         -3.6093879        3.733916242          5.8656510        1.554307033         3.80813115        -4.74817478          0.9967577         4.21335589        -3.79160251        -0.27816578         2.15737725         -2.0032367         -3.5666508        -0.60209057        -1.95764050        -4.09387535        -4.91121565        -1.31860793        0.004839387        -0.71339502         -0.6991190         -3.9212620         0.20648249          4.1143265         4.94718475         2.97327802          4.4147432        -1.74889853         -0.4990265         -5.8390450
WATANABE_COLON_CANCER_MSI_VS_MSS_UP                       -1.7007583         0.25210547        -2.98028816          4.3616661         0.78884983         0.07233832        -1.40118606         -2.8961949        0.004100867         -1.1888170       -1.104752765        -1.38781767         3.19210792         -1.1626383        -2.68443406        -0.86437807        -0.25770287        -1.21047088         -1.4287985         -0.5138995         0.58785731         1.62059758         0.58826582         2.11523939         0.95256194        3.100843936         2.98714276         -0.5977086         -1.5766500        -1.05054331          1.8346936        -0.50176549         0.33463179          0.9073378         3.12400300         -0.2618967         -2.0536422
> 
> proc.time()
   user  system elapsed 
 55.282   1.945  57.216 

GSVA.Rcheck/tests/test_zscore_newapi.Rout.save


R version 4.3.2 (2023-10-31) -- "Eye Holes"
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> 
> ## 2023-11-10  axel: simple test script for method z-scores, new API
> 
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    expand.grid, I, unname

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db


> library(GSVA)
> 
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
> 
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
> 
> p <- 10000 ## number of genes
> n <- 30    ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+             dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
           s1         s2          s3         s4          s5
g1  1.4171739 -1.3444519 -0.99052898  0.4203395  1.30716224
g2 -0.7281951  0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754  0.09779699 -0.6792548 -0.09124045
g4  1.0735382  1.3156255  0.15588330 -1.8079608  0.48531108
g5  0.7229884 -0.9162342  1.93982245  0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+                    paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> zscorePar <- zscoreParam(X, gs)
> zscore.es <- gsva(zscorePar, verbose=FALSE)
> dim(zscore.es)
[1] 100  30
> zscore.es[seq.int(min(nRowsToPrint, nrow(zscore.es))),]
               s1          s2          s3          s4          s5         s6          s7          s8          s9         s10         s11          s12        s13         s14        s15          s16         s17         s18           s19        s20         s21         s22         s23         s24         s25         s26         s27          s28         s29          s30
gs1  -0.397989121  0.63767552 -0.71152962  0.95681431 -0.39154705 -1.0418650  0.76943162 -0.22652269 -0.03794476  1.23795689  0.54741085  0.541307906 -1.3025217 -0.07350935  0.5617042 -0.110558260 -1.48434203  0.48341124  1.4582348818 -0.6596565  0.42366570 -1.18733982 -1.38666349  1.77213207  0.49521884 -0.54625805 -0.46923643 -0.326809131  2.03448230 -1.565153279
gs2  -0.292150055  1.00652251  0.59082177  0.60360826  0.09399124  0.3990216  1.16059005 -0.51857868  1.57864006 -1.82507931  0.27951753  0.015075493  0.7420740 -0.26993044 -0.1951051 -1.228360534 -0.29127936 -0.38907836  1.7217817461  0.4289776 -1.05871842 -1.92619800  0.16799779  0.27006041 -0.01617003  0.22027905  1.62510577 -0.140877183 -1.58374028 -1.168799069
gs3   0.286561399 -1.05214008  0.44954052  0.05225134 -0.27816203  0.5745265 -0.08816684  0.55254769 -1.29875323  1.56194900 -0.05237899  0.263111063  0.9526169 -1.98894869  1.9629224 -0.260586823  0.03510070  0.11049165 -1.0053564642 -0.7887344 -2.62545010  0.37942785 -0.80210329  0.63432226  1.52546755  0.14200823 -0.95287090  1.269227032 -0.32940645  0.770986212
gs4  -0.354767925  0.21855737 -0.54770518  0.57023369 -0.40119719  1.1654367 -0.85027787  0.05797497 -0.57666632 -0.19441172 -0.84753296 -0.201717192 -0.4443591  0.31037957  1.4397151  0.144981987  1.28913756 -0.76109926 -0.8188041253 -1.1193965 -0.34735329  0.02731708  0.47050049  0.36107874 -0.24978630  0.69621376 -0.34730205  0.335664905 -0.50390439  1.479089488
gs5   1.053567012 -0.90096227 -1.22439233  1.38286556  0.72832395  0.2446611  0.64214154  1.67034063  0.94014544 -0.56337436  0.13297430 -0.003270595 -0.4892865  1.04965180 -0.9017189 -1.422587378  0.25687151  0.34246303 -1.3100855881 -0.4117660 -0.56998370 -1.04747710 -0.59951317  0.38286581 -0.42463836  0.29869964  0.69420619 -0.224502898  0.01378260  0.259999076
gs6  -2.244409734  0.99135128 -1.25755227 -0.48107465  0.77088243  1.1587775  0.84165607  0.70800821  0.04455796  1.20866884 -0.08722013 -0.339734762 -0.3068380 -1.26475846  0.1691293 -0.016173483  0.08935879  1.04034445 -0.7302067427  0.3619944  0.09955336 -1.47161635  1.46668998 -0.57430525 -0.57827541  1.08697889 -0.36812846 -0.225673601 -0.63259981  0.540615686
gs7   0.052740026  1.67321048  1.06844511 -0.63335768 -1.29665110 -0.1715307 -1.66933194 -1.66163147  0.96745704 -1.98236849  0.39924531  0.780997272  1.5031445  0.82365265  0.7355819 -1.291690222  0.59198917  0.44201538  0.7748958150 -0.8715253 -0.42109173  0.38678646  0.62509742 -0.34088470 -0.73371942  0.45694938 -0.16347393  0.245014602  0.54802183 -0.837987628
gs8   0.128940466 -0.29023472  0.89066527 -0.61440040 -0.38274282  0.3546077  0.27907069  0.36742752 -0.96538900 -0.68424061  0.41316821  0.891427943  0.8562297 -0.82606670  0.9954917  1.271105299 -1.57441049  0.58613131  0.9237786732 -0.5526007 -1.00447106 -1.18216783  0.80591481  0.04182974  1.50238637 -2.48809418  0.67198869  0.329970369 -0.23288683 -0.512429049
gs9  -0.529924217 -0.50455633  0.14056762  0.82608534 -1.08452996 -2.4214825 -0.82702123 -1.51917889 -0.46117537  0.51536039  0.59351509 -0.477518222 -0.9141765 -0.36202472  0.2121035 -0.573687565  1.07691896  1.45448291  0.9987170368 -0.3781715  0.53631214 -0.44654865  1.24408983  0.30795693 -0.37080302  1.21990637 -0.38428269 -0.709115714  2.34614281  0.492038227
gs10  0.818321331 -1.51317539 -0.69457073 -0.49203352  0.36057893 -0.2397877  1.75081101 -0.06994105 -0.63367045  1.19094149 -0.90730458  0.767877575 -0.7928538 -0.06625141  1.5861559  0.979933067 -0.44783025  1.27989685 -0.4868701103 -1.0117896  0.94361547  1.85673623 -1.61731898  1.21625436 -0.28647246 -2.18059795  0.27744213 -1.003408010  0.30192017 -0.886608508
gs11  0.367678555  0.91252056 -0.42227266 -0.97087272  1.79158580  1.2585482  0.94342732  0.33332996  0.25752326  1.08956985  0.42462020 -0.463361537 -1.0340709 -0.62851508 -1.0342834 -1.514469249 -1.59087446 -0.08592467  0.5711694824 -0.2126554 -0.78142230 -0.16484959 -0.11708371 -0.06365675 -0.30699322 -1.78437695 -0.38348966  2.096264437  1.38197003  0.130964576
gs12  0.407633162  0.06089458 -0.03551973 -0.80557241  0.28472856  0.3839476  0.03138942  0.13026214  1.25696925  0.64914081  1.03413817 -2.014871071 -0.6371566 -1.64623803 -0.4174678 -1.889613999  0.17910813  0.02329786 -0.0009531196  1.3544298  0.64070445 -0.12299599  0.34538224 -0.04683912  0.06609172 -0.03387139  1.19121339  0.002288050 -0.67084599  0.280325902
gs13  1.117333034  1.17636696  0.90610556 -0.20339948 -1.76940395  0.6695672  1.67072725 -0.88508357  0.21042968  1.10554677 -1.20938609 -0.936796828 -0.5420542 -1.95749072 -0.1021446 -0.326335251 -1.38725541  0.03867057  1.2922253522 -0.2178358  1.11848269  0.61807105 -0.58824635  0.51758303  1.16189807 -0.11542606  0.56125057 -1.102475834  0.07801156 -0.898935092
gs14 -0.087991419 -1.48961560 -1.81093995  1.52077150  0.42263796 -0.2523003  1.81177614 -0.98653014 -0.44359835 -0.78718957 -0.27032118  0.208913565  1.4209980  1.20266088  1.0754392 -0.017917459 -0.55564302  0.04818988 -0.0639771402  0.5514408  0.12200747 -0.61335181 -2.18595402 -0.10832614  1.30303553 -0.18875480 -0.15271362 -0.366281115 -0.10674437  0.800279063
gs15  1.343950151  0.42076882  1.38439882 -0.88759686 -0.91178620 -0.4662795 -1.04143070  0.63814001  0.82957344 -0.29962403 -0.07941374  1.630590421 -0.5871337 -0.07434265 -1.5095501  1.553793983 -0.34571793 -0.82240473 -0.0947857521  0.8003060  0.21116056  0.32367880  0.86106297  1.65628788  0.97789380 -1.11080368 -1.05693195 -1.075624856 -2.14302463 -0.125154750
gs16 -2.280647404  1.45443048 -1.15615266  1.22715648 -0.91887150 -0.8774493  0.59718755 -0.53354106 -0.56650374 -0.69692215 -1.94787175 -0.263432001  1.8506749 -0.38045289  1.5196647 -0.171439192  0.23374260  0.12207975 -0.3457662199  0.8058231 -0.04857341  0.06274313  0.24285089 -0.52530011  0.36494819  0.51658411 -0.01130771 -0.356448130  1.77208671  0.310706625
gs17 -1.793915600 -0.76504524  0.63042343  0.52009464 -0.76953891 -0.6130846  2.30516686  0.87030325  1.22942353 -0.38676648  0.28786780 -1.294578572  1.0048342  0.34124188  0.6789841 -0.427903451 -0.26781132  0.36824855  0.1448156182  0.2312562 -1.65929393  1.39937404  0.85491251 -0.82632158 -1.70289841  0.74965589 -0.12891045 -0.156350687 -0.69636392 -0.127819267
gs18  1.076598555  0.66297942  0.31193924  1.21825571 -0.97634484  0.2376817  0.95228421 -0.69548369  0.64407889 -1.54705843  0.78530509 -1.141744986  1.0737459  0.20826231 -0.7801733  0.779895003  1.28313586 -0.72108935 -0.2461143875 -0.7458027 -0.38409736 -0.53680945  0.39463325  0.46243990 -0.97160166 -0.73933254  0.11490689 -0.850845941 -1.31226102  1.442617701
gs19 -0.932647493  0.36466764 -0.35976335 -0.48336730 -1.40727655 -1.7654296 -0.20079225  0.78943776  1.05075289  1.00527802 -0.38819134  0.067221765 -0.3143035 -0.09898034 -0.3791052  0.742819045  1.03125690 -0.29435736 -0.8584556405  1.5373474 -0.10243970 -0.45157605 -1.14712245 -0.58329174  0.09597807  0.98132256  0.98914383 -0.803965353  1.03267715  0.883162283
gs20 -2.507512451 -0.09179266  0.89256971  0.73127951  1.29936004  1.0227561  1.19748908 -1.12254621  0.39765236 -0.32497812  0.92840593  0.535525595 -0.6698568 -0.67309618 -2.7854267  1.470107881 -0.08598559  1.74783328  0.5261305573  0.1206040  0.50408329  0.08501165  0.83770748  0.10297851 -1.04236424 -1.27093846 -0.79581565 -0.156645031 -0.34413218 -0.528404617
gs21  1.590666101  1.21727966 -0.51796988 -0.70384659  0.47869886  0.6412920  1.08855268 -0.47402976  0.08376531  0.13287875 -0.58417864 -1.418465566  0.3586347 -0.06298446  1.0527743 -2.146897926 -0.23073419 -1.51825713 -0.0886423308 -0.8228190 -0.89776066 -0.01018669  0.03607537 -0.23848721 -0.91307940  2.16316601  0.88039149 -0.180082700  0.42559671  0.658650146
gs22 -1.314146576  0.56105707 -0.29581903  0.01879511  0.70153285 -0.4595619  0.79526977 -0.30610624 -1.59054925 -0.12272649  1.47363794 -0.919840374  0.3988845  0.50906124 -0.1078853  0.005275414 -0.80093636  0.02875750  0.1796627484  0.8606802 -0.14613823 -0.08254134  1.34492879  1.33240524 -0.72078684 -0.13081350 -1.79095355  1.829439862 -1.03960553 -0.210977661
gs23  0.007467771  0.87566015  0.10324376  0.43422509  0.89948175  1.4248760 -0.42838198 -0.63377944 -1.60531538 -0.81617333  0.71976579  0.178541229 -1.5026766  1.31351070  0.5908263  0.295870288  0.31272798  0.41614095  1.5239090790 -1.0149427  0.50905084  0.08055801 -2.05892070 -1.43447026  0.75255573  1.23995792 -0.53070949 -0.671543192 -0.97238791 -0.009068384
gs24  0.962632242  0.95541708 -0.19066384 -0.23175174 -0.76110030 -1.4063679 -0.89610030  0.66372973 -0.80965792  0.08779694  1.43555471 -0.290334626  0.2202661 -0.20314804 -1.7974438  1.986615879  0.30858557 -0.81071709 -2.1361827974  0.5564193  1.76375887 -1.03057351  1.32045107 -0.52316315  0.55080127  0.67747310 -0.41157504 -0.004477188 -0.66154101  0.675296303
gs25  0.750300473 -0.69054276  1.18919625  0.22555676 -0.89812453 -1.9043047 -0.08872006 -0.53073008 -0.25382802  0.61889062  0.54487413  0.150650635 -1.1560727  0.67452679 -0.4169377  0.301273856  0.27364471  2.12016724  0.2984327507 -0.7254619  1.57708274 -2.55299380  2.35308624  0.03326361 -1.15647532 -0.70205328  1.05030170  0.062511954  0.46103929 -1.608554943
> 
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+                     featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+                     sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+                                       grep("^REACTOME", names(c2BroadSets)),
+                                       grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+                collectionType=BroadCollection(category="c2"),
+                setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- zscoreParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+                       minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
                                                    NA19099     NA18523     NA19144     NA19137    NA18861     NA19116     NA19130     NA19131    NA19119    NA19152     NA19153     NA19140     NA19138     NA18522     NA19192     NA19193     NA19239     NA19238     NA19210     NA19201     NA19172     NA18870     NA18858     NA18852     NA19159    NA18855    NA19204     NA18501     NA19127     NA19098     NA19093      NA18856    NA18912     NA18517     NA18502      NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                  0.08200762 -3.52041732 -3.26174022  0.51755585  4.3317957  0.20731183  0.79679064  0.79926124  0.8990293 -0.3162241  1.37146559  1.28865093  0.08780809 -0.04487147 -0.91082622 -2.01743735 -3.12498579 -2.43416998  1.66792540  0.63671241  0.98429879 -2.77176425 -2.57368171  1.08251788  1.86537795 -0.2611243  0.3413125 -0.86055908 -1.49156413  1.32126944  2.69602243  1.710794035  0.8409827 -1.34346099  1.04123139  0.362705265
KEGG_CITRATE_CYCLE_TCA_CYCLE                     0.22642469  2.71693263 -0.10717960 -2.55590909  1.8299224 -0.47957924 -0.54472874 -0.02445334  0.9176705 -2.7381498  2.48189970  0.83060592  0.38079534  3.38221199 -0.32877740 -2.83603934 -4.22277480  0.30241154  1.04250419  1.46120065 -2.03473559 -1.21891964  1.08436248  1.06426425 -1.55401694 -0.5226624 -1.2189195 -0.45981366 -1.44418236 -0.97635055  0.50837155  0.687584202  2.5479218  0.26221667  2.58838008 -1.048488516
KEGG_PENTOSE_PHOSPHATE_PATHWAY                   1.36770713 -2.36222774  0.04423311  0.12728501  4.5866555  0.73826068 -0.30430005  1.12280301  0.7386334 -0.4741849  1.94803182  0.77746818 -0.21649571  1.53618820 -1.14034304 -2.06467802 -3.35703927 -0.52856032  1.23074711 -0.38012652  1.09162981 -1.97458243 -1.97155134  0.40676902 -0.11013586 -0.8840621 -0.1723332 -0.55469059 -1.82128559 -0.27395469  0.21881375  1.100739928  0.2091012 -0.73264959  1.63276978  0.445364274
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS    0.24894806  1.15822465 -0.63403859 -2.85893527 -0.1383472 -0.23236162 -0.85909142  0.52113731  0.4042918 -1.2811704  1.65377601  1.05051126 -1.44312727  1.72029902  0.59548843 -1.29956124  0.13453374  1.14525277  1.29207698  0.58036810  0.53523531 -0.44979114 -0.57051676 -0.15789451 -0.25900848 -2.1421868  0.4292179  1.66346748 -0.71371117 -0.01810125  0.12724512 -0.774738588  0.2843053 -0.03222607  0.34212600 -0.021697443
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM             0.09155076 -1.97525177 -1.45276746 -0.07481523  3.5602457  0.21410187 -0.46891224  0.48276577  0.8301800  0.2782034  1.76137958 -0.30167366 -0.36866461  1.40519024 -0.46806431 -1.89929335 -2.77414056 -1.44200425  0.06351456  0.43244830  0.47487440 -0.05968271 -2.47979046  0.88521908  1.45849373  1.4370859  0.7227373 -2.42689891 -2.32001921 -0.69902703  1.80940353  1.445144270  1.1884455  0.36808537  0.73860677 -0.436670241
KEGG_GALACTOSE_METABOLISM                       -1.50220635 -2.12210786 -2.26086463  0.19222532  3.7806514 -0.02135668 -0.06191917  0.04740533  0.3036345  0.8632324  0.86542561  0.79337892  0.94383717  0.64846184 -1.52736862 -2.10108047 -2.57431539 -2.81169968  1.46044938  1.54579783  2.08963590 -1.37567056 -3.06980601  1.26834691  2.35203893 -1.1214375  2.0145262 -0.70745876 -3.08391089 -0.38893891  1.12194963  1.625915928 -0.1365118 -0.66174770  1.84065605  1.770831772
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM           1.62312696 -0.15873213  0.21618956  0.46858637  0.9166095 -1.04599221 -0.27045669  1.11594251 -0.7483182 -0.1238161 -0.08764850 -0.32826008  0.34447096  1.24438098  0.61296527  0.15432850  0.45526120 -0.36519590  0.20463352  0.04105416 -3.40788046 -0.10615080  0.03162673  0.30778305  0.76679284  0.7047822 -2.6927801 -0.49668598 -0.74070175 -0.19230287  0.78253260  0.019056184  1.1861060  0.56044201 -0.99809984  0.006350524
KEGG_FATTY_ACID_METABOLISM                       1.35637843  1.25200293  1.07298339 -1.71740038  2.3901222 -0.36157315 -0.61828083  2.30667544  1.7661146 -1.3820937  1.13392622  0.56871041 -0.79388010  1.09003603 -0.36094837 -2.90971040 -1.94439447 -0.01160654  1.33989630  0.15215352 -2.89938246  0.22556399 -0.77232732  0.57215286 -1.83412952 -0.7752354 -4.1289987  0.02530249 -0.63474809 -0.08583303  1.30223207  0.651511781  4.0322588  0.16603308  0.29172425 -0.465236301
KEGG_STEROID_BIOSYNTHESIS                        1.36553599 -0.12013577 -3.08293491 -1.34327805  1.3358376 -1.11364214  1.86689706  1.85283136  1.5670901 -1.7482283  0.54388973  0.03810215 -1.44328919  1.85735478  2.10172330 -2.62881691 -2.32801957  1.24532010 -1.02033468  0.69913015 -0.29822576 -1.97008651 -0.19118335  0.33269001  1.52165526 -2.1837464 -2.2547570 -1.83792686  0.06447423  2.18187799  0.88568269  1.120120992  1.0123686  1.94734636  0.53060126 -0.505924347
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS             -0.08350356  0.59893449 -0.18051314  1.46849025 -0.5398104 -0.94926659  1.14314746  0.90284639 -0.9560743 -1.7658533 -0.74679073  0.45581317 -0.76088516  0.75908154 -0.92291196 -0.68856752 -1.36785514  0.55938543 -1.85379029  0.65684292 -1.41481016  0.37705982  0.35137739  1.54211015 -0.08423593 -0.8595118 -1.1072458  1.75411782  0.91579317  1.05847124  1.52536833 -0.703220257  0.4891219  0.94531073 -0.02348034 -0.494945723
KEGG_STEROID_HORMONE_BIOSYNTHESIS                2.15700695  0.10244885 -1.53755271  0.84766905  0.5856113 -2.09650629  0.33261928  0.53843117 -0.6734007 -0.4685420  0.95573879 -0.82998047 -1.41476255  0.62639471 -0.09031677 -0.08950504  0.11011468 -0.44476912 -0.28512821  0.29866023 -1.98900643 -0.24411969 -1.43499147  0.86760041  1.02524276 -0.5932665  0.1374354  0.21201533  0.34436727 -0.41016807  2.07943956  0.425593065  0.3466719  1.06122025 -0.79768577  0.345420779
KEGG_OXIDATIVE_PHOSPHORYLATION                  -4.63240554  6.67049017  3.29453045 -5.55357439  0.5496431  1.77914583 -1.36568735 -0.24226839 -0.9307871 -1.1747541  4.67610019 -0.89434533  0.91778294  3.85769951 -0.94501694 -4.63557269 -3.61619441  2.54955115  3.68603811 -2.72776413 -3.86124115 -1.43398278 -0.68050376  3.04817148 -2.44714051  2.1306825 -0.6471011 -2.51904678 -2.43888735 -1.23953015  0.48985662  0.954496754  3.8663223  1.61356139  4.95225010 -3.050518657
KEGG_PURINE_METABOLISM                           0.62601378  0.18764292  1.73576348 -0.39598650  2.8634149  1.74410636  0.80345344  0.21606301 -1.3228291 -1.6357118  3.37382979  0.50309725 -1.50193862  2.70460008  0.64046292 -2.91457181 -3.24668292  1.31429488  1.82156620 -1.17862270  0.22910565 -1.92894788 -2.19958482  0.95864285 -1.79749826  0.3013226 -2.0561912 -0.90114440 -1.30231555 -0.50822552  1.03537654 -0.062022288  2.3525705  0.47295983  1.48590730 -2.417920862
KEGG_PYRIMIDINE_METABOLISM                       0.68740186  0.09101204  2.69635278 -0.42133976  0.8010248  1.80959049  0.21392008  1.07077719 -1.3103447 -1.9575492  3.30744108  1.47682356 -1.85296082  2.34519272  0.79412795 -2.39568143 -2.29502648  1.96378220  1.42298942 -0.45658368  0.59630261 -2.36440463 -0.67804226  0.66537108 -2.65018728  1.2139181 -2.3138877 -2.68945636 -1.24989873 -1.77690179  0.01581421  0.070503916  4.5215289  1.03102830  0.50944514 -2.892083563
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM  0.40749755 -0.34200633 -0.67837708 -1.23839426  0.6450508 -0.87406128  0.89718094  0.88623623 -0.5901204 -1.4540001 -0.87199772  0.42565207 -1.02900922  1.09092642  0.83055385  0.95392316 -1.75399991 -0.70209561  2.56557133  0.74972926 -1.57575278  0.32540715 -1.39589409  0.64504509  1.67331106 -0.4742681 -0.4768781  0.84809297 -0.83978189  0.95527769  1.45671942  0.108438034 -1.0078854  0.58026404 -0.78212513  0.041770444
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM     1.34480378 -3.30503462 -1.85282519  0.51114612  2.0581490 -0.56269049  1.33006959  0.04421460  1.1318004  0.3368706  0.50287384 -1.78230487 -0.50480571  0.94601805  1.04369734  1.71347618 -1.44995911 -2.43340216 -2.31170012  1.06556022  0.05794706  0.22204354 -0.97366673  0.37411217  1.72881970  0.3048721 -0.3882133 -1.42262378 -0.42158817  0.60165076  0.74800845  1.017367318 -1.4705719  0.31352222  1.51764940 -0.035286398
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM          3.05533939 -0.89909141  0.10954792  0.57235547  0.4626350  0.43289545  0.80738496  0.82828340  0.3856202 -1.2192401  1.88574795  0.99850668 -1.58048436  1.26624831  1.63212252 -0.17105083 -2.04406219 -0.17476728  1.10667030 -1.31693777  0.48580641 -1.58414785  0.05762645 -0.83033135 -0.25313737 -2.7494190 -3.0328378  1.09278033  0.12945747  0.94310449 -0.20656930 -0.008758587 -0.5489564  0.03192254  1.53794235 -1.202205950
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION   1.99685230  3.32822203  0.58345875 -4.52030235  0.3557779  1.04571821 -0.47089329  1.67689058  2.4018633 -4.7953730  4.07552302  0.75879243  0.62123432  1.51829109  0.78422115 -1.84905687 -1.97911844 -1.19127707  1.91957992  2.24311755 -2.31132941 -1.32123330 -1.89841999  0.56302584 -1.87052188 -2.8145421 -5.7964707  2.02162198  0.16550354  1.15166897  0.62682088 -0.514715091  2.6508192 -2.05463411  2.71049379  0.188390686
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS  1.21309346  1.03875454 -1.40361861 -2.52868933  0.4749534  0.80310065 -0.98833939 -0.71560160  0.3172929 -2.7148765  2.17790950  0.73901374  0.25849033  1.55020704  1.20997178 -0.08496525 -0.53778049 -0.39412463  0.91390937  1.51429190  0.98942311 -0.15970919 -0.70389239  0.07882245  0.51719734 -1.0064894 -0.3389961 -0.74168366 -1.24385664 -1.12735156  0.43249880 -1.443631927 -1.1247770  0.97292321  2.74297956 -0.686449461
KEGG_LYSINE_DEGRADATION                          1.27862971  0.71944399  1.63186710 -0.15625854  1.1239366  1.48957540 -0.71067310  1.03036572  1.0590009 -1.3259578  1.96846254  0.83164708  1.37283618 -0.32318559  0.82246557 -1.99572277 -1.13322958 -0.74814377  0.55359396  1.33240395 -0.03241343 -1.11966697 -0.40789253 -0.99695879 -0.31423848  0.5315305 -3.3596078  0.11542448 -1.01289512 -0.45023277 -0.42490054 -0.226806423  0.8458865 -1.67164998  0.99545026 -1.292086374
KEGG_ARGININE_AND_PROLINE_METABOLISM            -0.15234479  0.69098240 -0.76904212 -0.91208540  2.2065375 -1.38716533  1.98078525  0.27213689 -1.1158975 -0.9181385 -0.25718855 -1.95804902 -1.12474003  1.25322167  0.53928573 -0.73049153 -2.14409282 -2.25112459  1.25901808 -0.05875601 -0.95521014  0.40928361 -2.08064840  1.77638819  3.15870419  0.6818472 -0.8337812 -1.63164697 -0.97781157  1.68806097  1.53083443  1.557264638  0.1741774  1.04524198  0.46754689 -0.433102466
KEGG_HISTIDINE_METABOLISM                        2.68245243  1.47002186 -0.21440898 -0.53405078  2.0496709 -0.61763413 -0.26832178 -0.37983061 -0.5973106 -1.0657640 -0.90612550 -0.21298139 -1.00379460  0.17915007  0.94116346  0.18701698 -0.07179808  0.76376118  0.27104980 -0.74947548 -0.51319501  1.37082775 -0.09200211 -0.40229269  1.15117499 -1.9075314 -2.5648368  1.27744182 -1.25796002  1.29042314  0.68066731 -1.188354315  1.0593628  0.41174254  0.03668128 -1.274939998
KEGG_TYROSINE_METABOLISM                         1.91319390  0.74537191 -0.21049549 -1.42486425  0.5137825 -0.64566994  1.25615471 -0.66586315 -1.0869967 -0.7914632  0.10529750 -2.04374233 -1.41200636  2.03136776  2.15096014 -0.71526488 -0.41213522  1.77566582 -0.93917591 -1.12144350  1.31645784  0.85531594  0.03889139 -0.64170442  0.13590477 -1.9150054 -0.9753372  0.62223967 -0.54517272 -0.39983433  1.31049742 -1.405758842  0.7396993  2.28797364  0.70968153 -1.156521954
KEGG_PHENYLALANINE_METABOLISM                    1.71871162  0.85028780 -1.30449583  0.02082110  0.4768936 -1.66932255  1.68462411 -0.37651941 -2.3786373  0.7308768 -0.47484731 -1.97769588 -1.05075764  0.71056611  1.08003616 -0.61325382 -1.15603061  1.11546195  0.64651489  0.26703259  0.95952300 -0.67322170  1.09967677  0.27680080  1.06176322 -1.2410279 -0.2930592  0.65188967 -0.04065992 -0.62699333 -0.09001084 -0.001369905 -0.7343008  1.97832734  0.54187752 -1.169481219
KEGG_TRYPTOPHAN_METABOLISM                       1.16300387  1.44923733  0.64807218 -0.54150723  1.8798625 -1.75904518  0.40200001  1.19892690  0.7528380 -0.8030061 -0.00259142 -0.37058216 -0.79497393  1.00982067 -1.00764660 -1.04581411 -0.91849620 -0.59010610  1.71370618  0.38679017 -2.82420827 -0.14129154 -0.09195268 -0.23903564  0.93135542  0.4710853 -2.9961143  0.43059167 -1.18463698 -0.21792140  0.89276830  0.137376030  2.7846734  0.56166925 -0.53510897 -0.749738309
> pickrellPar <- zscoreParam(pickrellCountsArgonneCQNcommon_eset,
+                          canonicalC2BroadSets, minSize=5, maxSize=500)
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esrnaseq[seq.int(min(nRowsToPrint, nrow(esrnaseq))),])
                                                 NA19099    NA18523     NA19144     NA19137   NA18861    NA19116    NA19130   NA19131    NA19119   NA19152    NA19153     NA19140     NA19138  NA18522     NA19192   NA19193     NA19239    NA19238    NA19210     NA19201   NA19172    NA18870     NA18858    NA18852    NA19159   NA18855   NA19204    NA18501     NA19127    NA19098   NA19093    NA18856    NA18912    NA18517      NA18502     NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS                 3.613776 -4.9679841 -0.49159131  1.17771731 2.7476858  0.9906586  7.8351036 2.3879352 -12.247507 5.1072799 -1.7088887  0.63969178 -0.43172043 4.310571 -1.08484087 -5.547877  1.76164051 -0.8898460  1.5516740  0.18384396  5.802682 -3.7757111 -0.84888911 -4.0044153 -2.8284060 -4.082546 3.4904554  -8.250833 -1.84490573 1.28570738 11.673596 -4.2948444 -3.9836382  5.0572394  0.389111698  1.27807521
KEGG_CITRATE_CYCLE_TCA_CYCLE                    3.477784 -4.3258387  0.10679683  1.15022124 2.7107418  2.7378566  6.9986362 2.9781870 -12.336655 3.6489484 -1.0391481 -0.52824121  0.65826573 2.792346  0.29220725 -6.488304  0.72250541 -1.4678365  1.2401595  0.68473909  6.985360 -3.7270434 -0.23551620 -4.2369070 -1.5168679 -3.622173 5.4307235  -7.795052 -2.44363904 0.63072187  6.965976 -3.1341445 -4.1118426  6.2243145  1.240638472 -0.66792044
KEGG_PENTOSE_PHOSPHATE_PATHWAY                  3.339370 -4.0330816  0.51583498  1.40649749 2.3302549  2.0374336  6.8119003 2.4065127 -10.353614 3.3243129 -1.0295482  1.11054456  0.15015971 3.222526 -0.22754631 -5.181391  1.31417726 -0.2722243  0.6939848 -0.36386838  4.818728 -3.5438041 -0.36599427 -3.3620882 -2.3822479 -2.812857 2.8927987  -6.781842 -1.39440389 0.65166045  6.613795 -3.4344536 -4.0261038  5.4529813  0.015849046  0.45574590
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS   1.344052 -2.2158240 -0.21175907 -0.53842579 0.7156543  1.5288896  2.5831229 0.9317288  -5.466600 2.2964636 -0.8651491 -0.50386448 -0.91065031 2.898462  0.03623637 -3.073694  0.20949331 -0.2369633  1.4088917  0.05340645  6.570503 -2.3938190 -1.06915911 -2.4866369 -1.0079189 -2.759769 1.9916084  -3.275961 -0.49396629 0.49476943  5.002457 -1.8388175 -1.2006148  2.8157552  0.127652664 -0.45955629
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM            2.631917 -3.4339405  0.76408579  1.94446913 0.3597460  2.0623149  5.8373764 2.2457127 -11.233068 4.4543105 -0.8609952 -0.10889232  0.29460916 2.556143  0.11638893 -4.873598  0.98963304 -0.2427547 -0.0727344  0.05007844  5.596166 -3.1119692 -0.66278612 -3.4164707 -2.3915290 -2.741625 3.6366017  -8.051503 -2.16851806 0.18545576  9.295116 -2.9409623 -4.3732252  6.2960637  0.230435983  1.13794800
KEGG_GALACTOSE_METABOLISM                       1.982906 -3.9655472  0.61138910  1.15467260 1.6497432  0.8209315  5.2419040 2.1089802  -9.470991 3.7134731 -0.5181230  0.27522867  0.47877266 2.465661  0.52640555 -4.480509  1.01519660 -1.0516291  0.7645887  0.11440946  4.035460 -2.7583348 -1.29899318 -3.1760242 -0.7767365 -1.936233 2.8326448  -6.897092 -1.60000462 0.14907466  8.487595 -3.6464832 -3.5973961  5.0170353  0.116352490  1.61167165
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM          2.062532 -1.7226116  0.04676367  0.09733945 1.3732660  0.6312735  3.1964202 1.1698729  -4.661225 3.5280417 -1.0282684 -0.24234280 -0.15789395 3.398797 -0.27367316 -2.285976  0.59113894  0.1038181  1.7998289 -0.70562100  1.466847 -1.9910010 -0.43593836 -1.5128138 -0.6582237 -2.253523 0.1210538  -2.828518 -1.52381952 0.63908058  3.312295 -0.9165812 -1.5677085  1.2962335  0.006141184 -0.07500485
KEGG_FATTY_ACID_METABOLISM                      3.386727 -4.2988297  0.06235647  0.58211164 3.3131963  3.0678691  7.0037479 3.2012797 -11.277464 4.2927549 -1.4335746 -0.45941305  0.29576869 5.354193  0.02688667 -5.924900  1.13628254 -1.0545026  0.3870266 -0.12197680  6.536312 -3.4052486 -0.74006237 -3.1208879 -3.6370863 -4.832566 2.5697139  -7.724517 -2.04579965 1.96532286  8.388591 -2.7458801 -4.0057123  4.2475503  0.401532299  0.60919695
KEGG_STEROID_BIOSYNTHESIS                       3.656540 -2.2721186 -1.57781964 -0.72604499 2.6915557  2.7253367  3.4859428 2.1396122  -7.766563 0.3563763 -1.7757330 -1.54337991  0.07930328 1.934096 -0.40859022 -3.366802 -0.91869676 -1.4728893  0.1800936 -0.22016331  4.432150 -2.6588099  0.96699753 -3.0431456  0.2835885 -1.981831 1.9816759  -5.436519 -1.29757797 0.75871060  6.245049 -1.8776229 -1.5097635  5.8384179  3.033017936 -0.93439173
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS             1.116348 -0.9463790 -0.45604407  1.85063315 0.8106916 -0.3276203  1.2722726 1.5051284  -3.911297 0.4279352 -1.1991834  0.27030319  0.37304589 1.394388 -0.30774860 -1.744298 -0.92604666 -0.4823653  0.6953440  0.31728853  3.213363 -1.1520835 -0.44496503 -0.7902377 -0.8179018 -1.481037 0.8903110  -2.713066  0.11460137 0.99717578  3.970424 -0.9784062 -1.0879326  0.8027559  0.375701324 -0.63109969
KEGG_STEROID_HORMONE_BIOSYNTHESIS               2.480574 -2.2365775 -0.76345941  1.00478856 0.6737178  0.9885282  1.2763885 1.3246518  -5.234984 2.4601178 -1.4631961 -0.46795704 -0.10691565 1.885405 -0.83051072 -1.461525 -0.76902369 -1.9770725  1.6275719 -0.31312275  3.542358 -1.2925407 -1.34198406 -1.8121874  0.4845320 -1.476588 1.6850644  -3.134337  0.07214458 0.57869417  5.589447 -0.1789734 -1.8021160  1.3544518  0.029050681 -0.39441569
KEGG_OXIDATIVE_PHOSPHORYLATION                  4.599553 -6.7100059  0.42751863  1.23309432 3.6403868  7.3503379 11.9441178 4.5820577 -22.111947 6.7108308 -2.6602605 -0.07351686  0.54111443 5.562369 -0.51723640 -6.354949 -0.32498263 -2.1480812  2.6116772  0.93083606 13.369164 -6.1648449 -1.26630351 -8.0783946 -5.1518001 -6.967977 5.0669407 -14.885391  1.28479521 1.01972315 14.812577 -5.0108056 -4.7390139 10.5574156 -1.074527837 -2.00447078
KEGG_PURINE_METABOLISM                          6.220789 -7.3332881  2.16396498  2.57568871 3.9859659  5.9240050 10.3558058 5.7052135 -22.077635 6.8238021 -3.0415523 -0.54372207 -1.11552134 6.029539 -0.46629110 -7.154343  0.67053421 -2.8913745  4.9291899  0.29117744 13.403968 -7.1225909 -2.44539633 -8.3994983 -2.7797096 -6.288009 7.2046295 -14.113059 -0.82453646 2.33187623 12.429260 -5.8244919 -6.9103465  9.8373238  0.195600901 -1.74696832
KEGG_PYRIMIDINE_METABOLISM                      6.251783 -7.3004492  2.45514238  3.55758788 3.5294787  6.1695147 10.5996032 5.4341495 -20.035750 6.8378927 -2.6453473 -0.25241143 -1.71619115 6.033213 -0.02466917 -7.150940  0.78178056 -2.2034922  2.5335758  0.25118554 10.327172 -6.6221964 -1.55381413 -7.3268938 -4.5723746 -5.782497 6.6734213 -12.451852 -0.73080869 2.09920973  9.852821 -4.1746574 -6.4184518 10.0207656 -1.585732321 -0.85976870
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 2.224928 -2.5175231  0.31954322 -0.05577043 3.0724152  2.4451896  2.5921602 2.1124348  -8.210483 2.8724531 -2.1070978 -1.60741186 -0.68246497 2.199909 -0.19364540 -3.650181 -0.42907746 -1.8261277  3.0553026  0.60745873  8.136535 -2.2790936 -1.58939303 -3.1084949 -1.7070042 -2.761089 3.4866388  -5.033765 -1.82076593 1.96304371  5.189870 -1.6042160 -2.6184510  2.5338460  1.312164296 -0.32183720
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM    2.999856 -3.4375039  0.89916682  0.63033836 2.4687629  1.9603347  1.1901481 1.6342611  -6.972969 3.0118818 -2.0881152 -0.72779749 -1.62320621 3.334605 -0.62335248 -2.686378 -0.91324037 -2.4721889  2.3887953  0.02658081  6.061305 -2.0460961 -1.20709007 -2.7982678  1.6860733 -2.621328 2.2711386  -5.897327 -1.23629767 3.63007666  3.537552 -2.4197078 -2.4758398  2.1078716  2.260659728  0.14729905
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM         4.528253 -4.1049604  0.95473848  2.35554742 2.7822856  2.4088547  4.0580919 3.0774039  -9.706246 4.2374134 -2.1616616 -1.01364410 -0.94299011 4.890240  0.03792379 -4.658464  0.24416843 -1.9253826  1.9851437 -0.79513338  5.959851 -3.1596842 -1.27828378 -4.1484755 -0.6797800 -3.179783 2.6697157  -6.646975 -1.44841945 2.43818842  4.976755 -2.7140771 -3.0367858  3.6516496  0.249454763  0.09506715
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION  3.578068 -5.2126760 -0.06582990  1.05028056 3.1175359  2.9255891  8.6648883 2.3315356 -13.262600 4.3087913 -0.4353979 -0.65613429  0.66965563 6.611628 -0.05894749 -6.337658  0.72653584 -0.9627796  1.2156060  0.23131911  7.440367 -4.5184377 -1.26578230 -3.5938565 -3.1877200 -4.678520 3.2011377  -8.745689 -2.57894300 1.66411861  9.113690 -3.2824421 -3.9956024  4.9755314  0.821735158  0.19100324
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 2.540325 -2.5580006 -1.05293097  0.95062670 2.7166826  2.4195780  2.5974731 1.1984907  -6.563815 1.1393911 -0.6535133 -0.53905503 -0.48018704 2.677603 -0.01257593 -2.979565 -0.07920138 -1.4780887  0.6527642  0.82805025  4.578221 -2.3827049 -1.46480651 -2.3355377 -0.5622099 -2.138416 3.8006165  -4.314880 -0.76030110 1.13881051  4.554075 -2.4839790 -2.0330791  2.0076049  0.891015248  0.18152038
KEGG_LYSINE_DEGRADATION                         3.602131 -5.1825796  2.10404410  1.03465213 2.2325113  3.8859631  6.2068738 3.2557411 -13.475952 4.4676256 -1.5475372 -0.64332512  0.30278276 3.096102  0.80316244 -4.861363 -0.16047923 -2.7961166  3.1711096  0.15946804  7.862459 -3.9302227 -0.46045256 -4.2726251 -0.8764999 -3.201900 3.8283383  -9.229505 -1.76236481 0.80665042  7.238060 -3.3994653 -5.0360166  5.6878045  1.220045863 -0.12912036
KEGG_ARGININE_AND_PROLINE_METABOLISM            3.552908 -2.6014549  0.25403717  0.44467074 2.9611366  2.7482330  5.2593925 2.8596838 -11.003736 4.4014280 -1.4301706 -1.48503133 -0.53070060 4.554944 -0.84220810 -4.833547  0.25503808 -1.8556128  2.1043602  0.08116681  7.166741 -2.6433864 -1.27027071 -3.8686066 -2.0615804 -3.311451 3.5978009  -7.755397 -2.32827010 2.16085780  7.856669 -2.3568083 -4.1579194  4.1342672  0.563638193 -0.62082177
KEGG_HISTIDINE_METABOLISM                       2.377756 -1.5661914  0.96968517  0.67672158 0.9721192  2.3359869  3.2557159 1.0090144  -7.185205 3.1549802 -1.8899941 -0.60468775 -1.07159899 2.157091 -0.57746861 -2.782320  0.04684621 -1.1830784  1.5261956  0.19975447  3.864136 -1.8653606  0.09025289 -2.5738520 -0.6662499 -2.626624 0.5408687  -4.116989 -0.76704574 0.94226265  5.226687 -1.5137978 -1.9567396  3.5069890  0.784552904 -0.69041273
KEGG_TYROSINE_METABOLISM                        1.678686 -2.8624559  0.11380858  0.96294524 0.6770510  2.7615384  3.4725219 2.3537463  -8.530014 3.5068974 -1.7874306 -0.61405904 -1.40109143 1.614691 -0.66315954 -2.873058  0.36251656 -0.9941132  1.1490792  0.76083067  7.367480 -2.0494605 -1.01357494 -2.6154799 -1.7935798 -2.941109 2.5428844  -5.886190  0.22349847 0.56447214  5.669252 -2.2344264 -1.0213345  3.1941475  0.652568301 -0.34807790
KEGG_PHENYLALANINE_METABOLISM                   2.090906 -0.6398089 -0.96814219  0.10793026 0.9964645  0.5346435  0.6255186 1.3708515  -4.156439 0.9251142 -1.8077444 -0.76133326 -1.10126175 0.105535 -0.33588778 -1.258697 -0.35343074 -0.9379906  2.7207387  0.00165670  6.070485 -0.5640568  0.14502636 -1.1017496 -0.7081219 -1.161937 1.3090258  -2.597788 -0.49159141 0.02963533  1.589456 -0.9849399 -0.2852917  2.7296313 -0.251299048 -0.88510761
KEGG_TRYPTOPHAN_METABOLISM                      2.427252 -1.8565270 -0.36746740  0.32340813 2.1446252  1.8352479  4.3807816 2.0802495  -8.862574 3.1187773 -1.1165949 -0.32613518 -0.01228540 3.252853 -0.62866265 -3.014655 -0.48220328 -1.8893938  2.7605496 -0.83247782  5.133392 -2.3976572 -0.27716429 -3.1951290 -0.5176048 -2.990382 1.8257622  -5.044709 -1.80260786 0.91193140  5.959211 -1.2696260 -2.5846251  3.4311657  0.932687520 -1.04941279
> 
> gbmPar <- zscoreParam(gbm_eset, brainTxDbSets)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
                    TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up               -0.08909934           -3.152221           0.8107079          -5.2069957           -1.033834           -3.508842          -3.1829696          -0.6973523            2.015886           1.1632330           0.8404895           -2.159491           -2.548436          -0.8250184          -3.4106404           -4.002532           -4.613817           -3.044947           -5.242683          -1.2277799          -2.5902555          -3.9951172           -5.281595          -0.1906933           1.3229285          -2.3332362           2.2376210           -1.582096           -3.701165          -1.7871696           0.1453581           1.3152286          -0.9330403           -3.939937           -3.847457           -2.256774          -3.6583197           -3.343534           -1.732189          -0.3798295           -3.595637          -2.2691422          -3.4280276          -0.6868929          -1.5292866          -3.6440129          -0.8287959           0.4759527          -3.1435814           0.6136584
astroglia_up                -3.10555037           -7.101899          -4.0708334          -9.6701263           -3.664210           -5.299715          -6.9344991          -2.4056788            2.838336          -4.0490130          -3.1252581           -3.831245           -2.365279          -7.0701428          -1.7311405           -3.642857           -9.353379           -6.868324           -6.498363           2.5117857          -1.8454742          -8.1922252           -8.284021          -8.5971607          -0.8126084          -2.3739610           0.8329655           -4.621603           -7.722374          -6.1625899           0.7790239           0.7748605          -2.9931959           -2.105014           -4.057559           -3.331656          -3.4418359           -4.645598           -3.835184           0.7608445           -4.037412          -3.3140937          -8.1346699           0.6228006          -1.9891070          -3.3462253          -1.0731883          -1.4644452          -5.1808878          -2.8928713
neuronal_up                  7.37537036            0.902553           0.3057596           0.2300378            6.512670           -1.073758          -3.5261610           3.0524882            3.747227           0.1086332           7.3042698           -5.441629           -4.460294          -4.1315377          -0.9454844           -3.971821            3.422017           -4.541850           -2.411690           0.8123934           1.3326064           1.2388876            1.226472          -1.2244988          -1.4490155           0.2784605           5.5226593           -3.202053           -3.079236          -2.3312546           0.4439339          -0.4968675           2.5700910            2.587650            4.151428           -1.103735           0.1977171            3.893207            1.635213          -0.4158050            2.809088          -2.6602840           3.1488241           3.7441383          -0.2328512          -3.6994980          -3.8924016           8.6663741          -1.6945566           0.3744679
oligodendrocytic_up          3.29318629            1.254525           3.2712757           2.7191887            5.272348            1.175787          -0.2208184           3.3361411            3.463337          -0.8905276           4.5060174            4.925995            9.254130           1.6478948          -2.4138339            2.381934           -4.283642            1.802069            2.652757           0.6540577           0.6721184          -0.2149802            2.097069           1.0987993           3.9911220           3.4783625           5.9792216            1.707458            5.240817           0.4118169           2.0783070           4.4474700           2.4108206            4.348025            1.816250            5.848493          -0.1675866            3.913055            6.890191          -0.1129943            2.247621           0.3634295          -0.8202027           3.2955322           5.6991646          -0.6973273           0.6332216           0.5563794          -0.7722805           2.2257859
                    TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up                -4.0501595         -3.58528280           -2.150553           2.6903341           4.4208691            8.164340           2.1478449            2.838322           2.5975997          0.37673200            2.838609            2.075690            3.310031           1.3772906           4.1679206            3.366810            1.771455           1.1231341          -0.3661421           4.8202400           1.8597821           0.2832633           -3.299052           0.4615451            2.080973          0.75936460            1.128923          1.91788210            3.565186           2.8923945            1.620005           3.9857385           2.1520939           1.5575374           1.4959032            4.756540           -2.867930          -0.6443480          0.85949798           -1.785971           -1.176208          -0.7720236            2.199689          -0.4467583         -0.06920086          -0.1063925          1.59512455           0.2113819            2.180979            1.594056
astroglia_up                 -7.8449103         -3.69159341           -5.755313           3.0432536          -0.4214884            3.141192           0.4343735            1.984018          -0.1593382          0.03139333           -5.837569           -1.925856           -5.373983          -0.4965235           0.8055162            1.604746           -1.688300          -0.5820614          -5.4221591          -1.9257791           1.7990137          -1.8344248           -5.126051          -2.2978494           -3.971752         -0.08022663            1.269094         -0.04203954            0.291440           1.2673922           -2.484940          -1.8906992          -0.3366926           0.1137957           1.2937214            3.049417           -1.620135           2.3199253         -0.15299389           -4.373301           -3.517849           0.7444723            1.008946           0.7440944         -1.30587497          -1.1595379         -0.12211222          -0.7345510           -1.016347           -2.525468
neuronal_up                   0.7621561         -1.58714007            3.908310           5.1544726          -2.8583933            6.461310           2.4198545           13.914963           4.5975953          1.16075755           26.315151            6.131003           28.314920           0.9021609           2.6534158           10.109527           -1.392535           2.0200464          12.5550187           1.4292865           0.5672497           2.9720049            5.488963          -1.8932872           22.021493          4.08113876            1.624494          4.29047134            1.231357           1.0326487           -6.201044           3.2394715          -4.5485246           3.5140611           0.8060133           -2.388428           -5.656942          -5.3246569         -0.02576302           -2.989774           -2.180673          -2.7829681           -1.709889          -4.0113452         -5.27955635           0.1081630         -0.65506207          -5.1568867           -2.899157            1.900477
oligodendrocytic_up           3.4473515          0.08207331            2.122737          -0.4139425          -3.6839021            1.784584           1.6375784            3.111439          -1.1400225          0.24599609            2.236097           -1.539376            1.530867           1.2539415           1.4258764            3.523489           -2.181047          -2.2383685          -1.0576358           0.2384092           4.2246382          -0.1492978           -3.327585          -0.7908182            2.860221         -1.23331168           -1.455083         -1.56496385           -2.848318          -0.4789735           -1.910726          -0.6964973          -0.9156850          -3.7150977          -0.1130542            3.021765           -1.968815          -0.8635538         -2.90146119           -3.962522           -4.266302          -1.8826848           -2.813841          -3.7335868         -2.67976967          -3.3860511         -0.08389153          -1.4103498           -1.328776           -1.187159
                    TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up                  2.676893          4.30587603          -0.1484128            2.121824            1.193762            0.216868            2.098520          -0.3590077           1.4924973           3.1318506           -1.885732            1.708314            2.657195            4.545553            2.912760           1.9804288            3.802850            4.534642        -0.003929236           3.2517485           -2.888534           0.1771372          -1.1738971           2.8936005           -2.743719           1.2918124          0.08247081           -1.203403           1.4767707           -0.304507           -2.321400          -0.4437532          -0.3035455           1.4292700           0.6915937           4.0222928          0.19722388          -4.5950920          -0.9341628           0.3305044           0.1631184          -2.8586504          -0.5955305          -0.2539437           0.8313484            1.589897          -0.7911376            1.293819            2.079665           0.9014619
astroglia_up                  -1.410315          0.04597652           2.5770285            2.311639           -3.398351           -1.272882            2.373027           1.6009710          -0.2377814          -0.0469951           -3.575104           -3.168532            2.258187            1.899525            1.815670           0.1310026           -0.363329            3.570761         8.762186646           3.2915183            6.806357           6.3444795           5.9779424           5.6455262            2.528754           3.0563019          8.59482813            2.857618           5.3890853            3.179268            3.523551           3.7860581           3.8898683           6.9126141           4.3234965           7.5338826          4.60504082          -0.2121851           4.2592086           3.3834519           4.3762196           5.9914008           5.4677275           2.1915212           6.4911546            2.848080          -0.7855700            4.469387            5.496258           2.8326382
neuronal_up                    2.935035         -4.33202655          -2.3779648           -4.899466            1.924114           -2.897353           -2.767796          -3.8811350          -0.3370994           1.1164572           -4.545340           -6.060301            4.539371           -3.571778           -5.669859          -2.6699004           -3.006828           -3.455450        -1.900261556           0.6429803           -3.745943          -4.3142406          -2.7433338           2.6788158           -2.270892          -1.1439441          1.03773052           -2.029232          -6.1026313           -3.833959            0.559603           8.2443008          -2.5442885          -0.3626451          -2.5297864          -0.5810968         -2.26408321           0.6219462          -2.1951042          -3.4844647          -2.0629756          -3.2574162          -4.6249237          -4.2837280          -2.9083139           -2.304073          -4.9578554           -3.231750           -2.616099           2.6652850
oligodendrocytic_up           -1.429602         -1.16836372          -3.3273872           -1.484285           -2.102452           -3.335235           -1.695018          -2.8550582          -5.1228981          -1.1518311           -4.754625           -2.497824           -1.200832           -3.091723           -2.826340          -2.3319305           -2.020322            5.901598        -1.869680552           1.5415212           -1.287606          -0.8869270           0.6441386          -0.9799234           -4.562924          -0.1648678         -2.00977500           -3.914152          -0.6328189           -1.448776           -1.641520           4.8529785          -1.1013767          -0.1757191          -1.5306714           0.6552283          0.05824521          -1.7220446           6.6503840          -0.2605514          -1.7376517          -0.6012265           1.1494110           0.9321423           3.3145489           -3.385071          -3.7834245           -2.604791            2.660582           1.3763185
                    TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up                -1.5182935            1.414137           0.6145721           1.3611626           0.9299387          -0.6118263          -1.9077298           -2.977643            2.354636            1.256214          -1.0446336         -0.03521543          -0.2048689          0.08255436          -0.5703374          -0.5160375           -4.393404         -0.04869947           1.0193142            1.716183           -3.050138           -2.968484          -1.4182898
astroglia_up                  3.6679577            2.016040           3.8365848           5.3857249           3.6519214           4.1911267           2.2371880            2.996960            3.653019            2.850722           5.3799630          4.07607902           4.5965300          3.82064210           6.8146847           2.5472498            2.787112          3.48964654           3.3631687            7.909505            4.609892            2.788675           1.2952133
neuronal_up                  -3.5923614           -2.462081          -3.0230934          -2.2989952          -2.9441875          -2.8335093          -2.8902359           -2.778339           -2.445036           -4.896693          -0.7803416          0.16600660          -2.5170378          4.64377108          -4.2430666           3.5077554           -2.229394          0.68892787          -4.1220154           -2.572970           -2.437011           -4.344700          -3.5499763
oligodendrocytic_up          -0.4309207            1.205395          -3.3004554          -0.2007412          -2.3954090          -2.6221966          -0.6024445           -1.075083           -2.183149           -1.983176          -0.3895268         -0.45898726           0.9638120         -1.89896706          -1.4509535          -0.1200174           -4.067190         -1.98215669          -0.5922569           -1.755122           -2.906155           -3.149109          -0.9366359
> 
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+                                 grep("_DN$", names(c2BroadSets)))]
> leukPar <- zscoreParam(leukemia_eset, cgpC2BroadSets,
+                      minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
                                                  CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP                       -2.3189547         0.55622710        -3.11198172          1.4986887         0.79561210         1.27047787        -0.65748275         -3.6475523       -0.938530423         -2.2124263        1.492202601        -0.73476415         1.14702413         -1.8556094        -0.10710987         0.62555189        -1.84985291        -1.99696364         -1.6391298          0.7733034        -0.76199840        -0.11481253        -1.54473797         2.90988107         1.91589932        0.306170802         1.84065500          1.0454556         -1.7550145        -0.64379309          3.1809700         1.66381825         0.85600132          1.5031001         5.27303344         -0.3741954         -2.3891628
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP                      -0.1437327         1.34145819         3.12030398         -0.9451609        -0.65236606        -0.75734866         2.49198413         -0.6960575        0.479216286          4.2298075        1.699907478         1.80608946        -0.55495287         -1.2596018         0.67756954        -0.22151006        -0.57450357         0.22116396         -1.9389978         -1.6951874         1.38964755        -0.02115285        -0.93820411        -0.54585990        -0.77666967        0.094771714        -0.46941562         -2.4584473         -3.2781747        -0.41248115          1.9550954         2.96291598         0.77692080         -1.1198979         1.01968846         -2.1157809         -2.6910370
WINTER_HYPOXIA_UP                                         -2.2032116         1.94192756        -1.01905531         -0.2262124        -1.70570515        -1.31370553        -1.53784382         -4.1896689       -0.573056157          1.3188203       -1.630985843         2.11056496         3.86978019          1.7943601        -3.47417711        -0.09511845        -1.03683603        -1.41318482         -2.0541609         -2.5022841         0.95884756         1.99489650         0.01912947        -0.40707157         1.49731005        1.876664626         0.82794692          1.3034511         -1.9570481         1.23100844          4.5355537         2.45428354         2.43716611         -2.4481408         1.95214281          0.4155076         -2.7518949
PYEON_HPV_POSITIVE_TUMORS_UP                               1.8425924        -0.90371747         4.42311845         -3.7133346         1.07235312         1.59420262         1.54184230          5.1765404        4.512483991          5.3940779        0.528141105         6.86588624        -5.27763956          0.5196579         2.48547689        -1.84517673         2.66475634         3.44169814         -0.7470868         -5.1281340        -0.05626604        -1.23659933         0.25586378        -3.15164039        -4.16550799        0.041309197         0.47627197         -2.3210603          0.1246063        -5.22630542         -2.5795122         3.27132937        -0.03055620         -2.0519735        -3.90153690         -3.1462161         -0.7499449
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP              -2.0355786         2.60368733         1.65952935         -0.2731903        -2.82481184        -1.60635471         0.40429957         -6.5356063        1.373085999          3.2217230       -0.004117969         3.12303563         1.37715940          4.3192977         0.04425356        -1.21708631        -2.06097063        -0.94940011         -2.9791103         -4.4507436         1.15163993        -2.13360896        -2.04857971        -2.73828950         3.09070632        0.890670934        -2.19450875          1.7569005         -2.1019689         1.35470426          5.2654387         2.89066529         3.53097016          2.9110126         0.45673634         -0.7116174         -4.5599727
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP                  -6.1743193         2.10626458        -9.93033191          5.5020838         1.24528029         2.76706915        -0.76977556        -10.1318343       -1.226965247         -0.2985038        3.204167870        -2.06583449         4.01539216         -1.4989300        -0.80243199        -2.09676668        -3.92339728        -4.76956131         -3.5492403          0.6307940        -6.10750595        -0.36445017        -5.33447764         3.97968003         1.06375876       -1.501968354         4.59460616          3.0050082         -5.2099545         4.59692879          8.4071865         3.02679350         4.62088574          4.2776647         8.40747357          2.6954767         -2.3902658
LU_TUMOR_VASCULATURE_UP                                   -2.3516037         0.23422156        -3.24709239          1.9002877         1.06371531        -0.31124003         0.64150436         -4.4921642       -0.429394270         -0.4708068        1.209418772        -0.53680406        -0.18120399          0.1020756        -1.17510637        -0.13495767        -1.60844266        -1.61180192         -0.2395109          1.6463378        -2.91072538         0.28004166        -1.85054840         3.12872425         0.81025980       -0.427636238         1.02779187          1.5058078         -3.8168552         3.69953701          1.2982542         1.83497935         0.73751145          2.3115023         1.90714553          1.9502801         -1.4935021
KORKOLA_EMBRYONAL_CARCINOMA_UP                            -2.0102420         1.77944838         0.71764392          0.7225229        -0.47650814        -2.94754400        -1.68662524         -2.7193614       -0.282629306          0.8789733       -0.663623433         2.48363943         0.58547469          0.9084250        -1.30090891         0.91028023         0.22038861         1.58879655         -1.9871067         -1.0238739         2.48127825         1.11685683         0.80172070        -0.88055998        -1.02367666       -0.170070225        -0.56110595          0.9707670         -0.6937145        -0.51027108          1.3912644         1.21188680         1.78787521         -2.5882821         0.35238902          1.0686185         -0.4521463
KORKOLA_TERATOMA_UP                                       -0.3532193         2.17997348         0.03956106          1.3024658         1.85511030         0.23121185        -1.71392644         -2.2452103       -1.891420902         -1.2620777       -0.745760801        -1.54879367        -1.14580035         -0.4412586         0.13971105         1.04541604        -0.18902172        -0.56554466          0.0430148          0.3175348         1.08482965         0.62953613         0.19987932         1.49131527        -1.44961377        0.238083305         1.05678681          1.2490852         -0.7551186        -0.06277113          0.4286523         0.11269812         1.05268675         -1.7303152         0.59079381          1.2819498         -0.4704426
KORKOLA_YOLK_SAC_TUMOR_UP                                 -0.1040637         2.99594415         1.31530981         -0.3081178         0.62832670        -2.42448384        -1.00992574         -1.6262212        0.163843219          2.4035673        0.155357913         2.06606337         0.24037257          0.4130723        -1.10335321        -0.70220925         0.89210405         1.60172761         -1.0474659         -0.7906492         1.09211241         1.15544503        -0.36703662        -0.60395345        -2.57074459       -0.583146941        -0.73629462          0.3110249         -1.7065781        -1.25258365          0.9935598         0.79136836         1.51933857         -2.7892840        -0.09963966          1.6070600         -0.5198466
KORKOLA_CHORIOCARCINOMA_UP                                -0.3744594         1.47839993        -0.77812840         -0.2217174         0.83857394        -3.22690712        -1.70821076         -1.8247392       -1.096790972          0.7766130        0.106430602         1.53596539         1.48267931          0.3337191        -0.10364576         0.33957176         0.78113867         0.08030119         -1.7081769         -0.9363552         2.19093776         2.26944769         0.71838354        -0.24247756        -1.29633819        0.701466602         0.09347977          1.4125416         -1.8054660        -0.61006004          1.4158132         0.45544767         0.58758936         -3.0940532         1.23411751          0.5310415         -0.3361331
KORKOLA_SEMINOMA_UP                                       -2.9340089         0.09586312        -0.67073745          0.4686024         0.58281055        -1.86617285        -1.39432462         -3.8666739        1.166840265          1.9282066        0.806977219         2.90705383         0.99184039          0.1234681        -0.96569590        -1.16396240         0.28761478         2.57697201         -0.8848146          0.8255735         0.58071491        -0.18386443        -0.64027729        -0.33107070        -2.65069999       -0.739030827         0.26850943          0.6218152         -1.5319993        -1.03372781          1.5970938         1.42233007         2.14424171         -2.9444395         2.36223981          2.5275209         -0.4847880
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP         -0.1871021        -2.72933254         2.10389786         -1.5218035        -0.24851512        -1.94879594        -0.11225920          1.3387953        2.092476554         -0.5027557       -0.734496247         1.48332203        -2.06908392          2.1504269         1.57346111        -2.67286549         0.55601780         1.75728633          1.0591640         -3.5172751         0.41769901        -0.15799519         0.10733345        -1.26412040         0.62132681       -1.068445939        -0.81184190          1.7795510          2.8672636         0.51834308         -2.2301655        -1.72721639         1.30982203          0.7498270        -2.26434985          1.7641941          1.5182121
HOLLMAN_APOPTOSIS_VIA_CD40_UP                             -0.7820872        -2.13675642         3.39698951         -2.1548508         0.90823798         1.87534780         1.18216325         -0.3454263        0.519486282          0.7495966       -0.702832818         2.65768682        -1.39601416          2.9377153         0.01460505        -3.73008343        -0.30955544         2.04220857         -2.8652428         -3.1013878         0.38820637        -1.85976238         0.14583211         1.54497828        -0.51769728        0.030388041        -1.27655961         -0.1068228          0.1140717         0.19735404         -1.8393420         0.06094494         1.18064262          1.7171987        -0.09629675          2.0372182         -0.4801540
LIU_PROSTATE_CANCER_UP                                    -2.7418994         0.36658204        -3.31691584          1.3184501         2.30781570         0.78372138        -2.49394355         -5.4987675       -0.822790802         -1.2417137        0.174898665        -0.25341599         3.10520813         -3.4272596        -2.36564481        -1.46486084        -3.27025426         1.45149707         -1.9796783         -0.2385052        -0.10360642         0.41913964         1.31326282         2.25499078        -0.48834592        1.569427440         3.08573035          0.6747347         -2.1158608         0.88924255          2.5723039         2.39831139         3.32890627          0.5872895         3.74319390          1.1868815         -1.7081250
LIU_SOX4_TARGETS_UP                                       -0.3751389        -1.95588700        -0.83556096          2.8406515         2.03541886         1.67651015        -0.06264359          1.0278755       -0.621726452          0.1542651        2.093682904        -1.12917548        -2.22483713         -1.1771779         1.46468782        -0.49621654        -0.06320445        -1.49441905          1.4408110          1.3723181        -2.65175416        -5.32222009        -1.90422195         1.32712098         0.41560025       -0.141050306         0.65594298         -0.6743251          0.5105999         2.58778466         -1.0269048        -0.06555656        -0.16265033          2.7736846         0.23669453         -0.9452083          0.7162302
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP             -1.2464061        -2.52190564         0.34481699          0.6136117         4.14525942         1.31851001        -1.50928145         -3.5261653       -0.376143666         -2.1419889        0.263685045         0.03051013         2.23927375          0.2887824         0.30432686         1.08666353        -1.81678277         2.91665062         -0.4815280          3.7840202        -1.28255238        -0.92708160        -1.47494702         0.36348866        -1.35695710       -1.365236115        -0.09332459          0.6773143         -3.3005646         1.08982967          1.3469267        -0.15650030         1.18988291         -0.1304936        -0.41848104          5.7424208         -3.6196334
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP                  -3.8776379        -1.06789926        -7.00642158          5.2446555         1.06812916         1.14091106        -1.23350873         -7.0151593        0.787783143         -2.2876206        4.506629996        -0.82513916        -0.50395314         -2.3986535        -1.14874866        -3.70233709        -0.71755286        -1.99280231         -1.4519194          1.8781710        -5.50515340        -3.26577909        -6.14460283         3.77798602         1.26457017       -2.522562013         2.00592405          2.4181014         -3.8502790         6.01626665          3.2565317         1.33592939         2.78983801          6.8105203         5.47203316          7.8148200         -1.0710708
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP                  -0.5530494         0.91449001        -5.10684798          5.8892478         0.70327111         0.68010952        -1.35401240         -4.1731715        0.829970887          2.0186035        0.734848132        -0.53350919         3.00824815         -1.7128629        -2.31656387        -1.10739140        -1.78453464        -1.33346346         -0.1610865          0.1636164        -4.61596682        -0.04388835        -2.22820486         3.50293537         1.08838500       -0.856531524         1.18347365          0.7537940         -3.2931554        -0.12534415          2.1550084         1.22544443         0.02188584          3.0547016         4.00283815          0.7785386         -1.4098262
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP                      -1.0842740         1.15191033         0.19359086         -0.2177736        -2.01743872        -0.35397625        -0.86551082         -0.6587418       -1.482192451          0.5834861        0.095377824        -0.80250318        -0.03850151          0.1414836        -1.48102277         0.70702073         0.54101179        -1.89001468         -0.1428820         -0.2992931         0.06876902        -1.27262670        -0.73299530         0.15317029        -0.21894175       -0.995729217         0.31049138          1.3867304          0.8623611         2.09995277         -1.6338695         0.65923937         0.40301566          2.6698444         1.87944620          0.4256969          1.8556888
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP                       -0.6904303         1.93458550        -1.99458125          1.5799006        -0.04746809         1.35845690         1.35954571         -1.3239543        0.183594189         -0.7304046       -0.867718542        -0.16037922         1.01551852         -1.2458131         0.36381625        -0.77975659        -0.36807781        -0.37384028          0.5956824          1.1883224        -0.48945985        -0.09633758        -0.76459822         0.07532145        -0.07071889       -0.592753031         0.03215539          0.4208453         -1.3262166         0.06108885          1.8490292        -0.26820419        -0.03938847          1.1315785         2.00315374         -0.7778437         -2.1446504
FRASOR_TAMOXIFEN_RESPONSE_UP                               0.5413132         1.28746036         1.36441186          3.3368271        -1.31891545         1.57406315         0.31091232         -1.8851886       -1.508855984         -0.2751830       -0.859463551        -0.54855067         3.08124648         -2.9190068        -2.21050219        -1.68670629        -1.28382294        -0.29745413          0.4018516         -0.7913413        -2.31590360        -2.18097162        -0.89954411         1.44692469         0.04672709       -0.343429133         0.79945007          0.2049267         -0.4953848         0.11145147          0.2050700         0.26420024         0.55065832          1.2372609         3.15265775          1.3700061          0.5328047
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP                     -2.6864978         3.43756903        -8.37492717          3.4513206         0.39310486         2.00425397        -0.88377471         -6.5962386       -1.122346365         -3.3992922        1.699856481        -1.83778409         1.82943931         -1.0046215        -2.58511818         0.68047190        -2.39298391        -4.23623360         -0.4038435          3.2643617        -5.42149983        -0.47681907        -2.08912701         3.41957446         0.43726984       -2.000731185         4.26612070          1.7425539         -3.2522439         1.90242944          7.7104250         1.33084413         0.94700410          2.9575476         6.54983238          1.8646617         -1.1245584
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP                       0.7708646         1.64610911         2.90389826         -1.5098526         0.68514559        -0.62856125         1.44344048         -3.6093879        3.733916242          5.8656510        1.554307033         3.80813115        -4.74817478          0.9967577         4.21335589        -3.79160251        -0.27816578         2.15737725         -2.0032367         -3.5666508        -0.60209057        -1.95764050        -4.09387535        -4.91121565        -1.31860793        0.004839387        -0.71339502         -0.6991190         -3.9212620         0.20648249          4.1143265         4.94718475         2.97327802          4.4147432        -1.74889853         -0.4990265         -5.8390450
WATANABE_COLON_CANCER_MSI_VS_MSS_UP                       -1.7007583         0.25210547        -2.98028816          4.3616661         0.78884983         0.07233832        -1.40118606         -2.8961949        0.004100867         -1.1888170       -1.104752765        -1.38781767         3.19210792         -1.1626383        -2.68443406        -0.86437807        -0.25770287        -1.21047088         -1.4287985         -0.5138995         0.58785731         1.62059758         0.58826582         2.11523939         0.95256194        3.100843936         2.98714276         -0.5977086         -1.5766500        -1.05054331          1.8346936        -0.50176549         0.33463179          0.9073378         3.12400300         -0.2618967         -2.0536422
> 

Example timings

GSVA.Rcheck/GSVA-Ex.timings

nameusersystemelapsed
computeGeneSetsOverlap0.0520.0000.052
filterGeneSets000
gsva0.3490.0040.353
gsvaParam-class2.0800.1162.197
igsva000
plageParam-class1.0790.0161.095
ssgseaParam-class1.1010.0161.118
zscoreParam-class1.1440.0281.172