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BioC 3.0: BUILD report for genefu on zin1

This page was generated on 2015-04-10 09:39:21 -0700 (Fri, 10 Apr 2015).

Package 347/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 1.16.0
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/genefu
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded [ OK ] OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: genefu
Version: 1.16.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data genefu
StartedAt: 2015-04-09 18:43:48 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 18:44:41 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 52.6 seconds
RetCode: 0
Status:  OK 
PackageFile: genefu_1.16.0.tar.gz
PackageFileSize: 4.462 MiB

Command output

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###
### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data genefu
###
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* checking for file ‘genefu/DESCRIPTION’ ... OK
* preparing ‘genefu’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* building the PDF package manual
Hmm ... looks like a package
Converting Rd files to LaTeX ......
Creating pdf output from LaTeX ...

This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian)
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entering extended mode
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh
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(./Rd2.tex (/usr/share/texmf-texlive/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
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*hyperref using default driver hpdftex*
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Package hyperref Warning: Option `hyperindex' has already been used,
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\T1/ptm/m/n/10 Kains \T1/fi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/fi4/m/n/10 <markus.schroeder@ucdconnect.ie>  
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 []  \T1/fi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[] 
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[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
omics Con-sor-tium us-ing Affymetrix hgu133plus2
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 []\T1/fi4/m/n/10 fuzzy.ttest(x, w1, w2, alternative=c("two.sided", "less", "gr
eater"), check.w = TRUE, na.rm = FALSE)[] 

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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
[14]
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[][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
[]$http : / / www . nicebread . de / blog / files / fc02e1635792cb0f2b3cbd1f7e6
c580b-[]10 .
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 []\T1/fi4/m/n/9 randst <- apply(rands, 1, function(x, xx, ww1, ww2) { return(f
uzzy.ttest(x=xx, w1=ww1[x], w2=ww2[x])[2]) }, xx=xx, ww1=ww1, ww2=ww2)[] 
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
 11\T1/ptm/m/n/10 (2):R18 
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 []\T1/fi4/m/n/10 map.datasets(datas, annots, do.mapping = FALSE, mapping.coln 
= "EntrezGene.ID", mapping, verbose = FALSE)[] 

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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
 and probes in columns,

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[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
 named "En-trez-Gene.ID",
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 []\T1/fi4/m/n/10 ovcAngiogenic(data, annot, hgs, gmap = c("entrezgene", "ensem
bl_gene_id", "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[] 


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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE 
[33]
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 []\T1/fi4/m/n/9 ovcAngiogenic.nkis <- ovcAngiogenic(data=data.nkis, annot=anno
t.nkis, gmap="entrezgene", do.mapping=TRUE)[] 
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Overfull \hbox (246.4477pt too wide) in paragraph at lines 1759--1759
 []\T1/fi4/m/n/10 ovcCrijns(data, annot, hgs, gmap = c("entrezgene", "ensembl_g
ene_id", "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[] 

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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE 
[34]
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 []\T1/fi4/m/n/9 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis, 
gmap="entrezgene", do.mapping=TRUE)[] 
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 []\T1/fi4/m/n/10 ovcTCGA(data, annot, gmap = c("entrezgene", "ensembl_gene_id"
, "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[] 
[35]
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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE 

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 []\T1/fi4/m/n/9 ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap
="entrezgene", do.mapping=TRUE)[] 
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 []\T1/fi4/m/n/10 ovcYoshihara(data, annot, hgs, gmap = c("entrezgene", "ensemb
l_gene_id", "hgnc_symbol", "unigene", "refseq_mrna"), do.mapping = FALSE, verbo
se = FALSE)[] 

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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE 
[37]
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 []\T1/fi4/m/n/9 ovcYoshihara.nkis <- ovcYoshihara(data=data.nkis, annot=annot.
nkis, gmap="entrezgene", do.mapping=TRUE)[] 
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[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the 
gene ex-pres-sions (see [][]\T1/fi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ). 
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 []\T1/fi4/m/n/9 tt <- data.frame(matrix(NA, nrow=3, ncol=3, dimnames=list(1:3,
 paste("column", 1:3, sep="."))), stringsAsFactors=FALSE)[] 

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 []\T1/fi4/m/n/9 tt <- setcolclass.df(df=tt, colclass=c("numeric", "factor", "c
haracter"), factor.levels=list(NULL, c("F1", "F2", "F3"), NULL))[] 
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[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][] 
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
 11\T1/ptm/m/n/10 (2):R18 
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
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[][][]\T1/fi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
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[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
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\T1/ptm/m/n/10 Kains \T1/fi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/fi4/m/n/10 <markus.schroeder@ucdconnect.ie>  
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 []  \T1/fi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[] 
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[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
omics Con-sor-tium us-ing Affymetrix hgu133plus2
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[][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
[]$http : / / www . nicebread . de / blog / files / fc02e1635792cb0f2b3cbd1f7e6
c580b-[]10 .
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
 and probes in columns,

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[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
 named "En-trez-Gene.ID",
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se = FALSE)[] 

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[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the 
gene ex-pres-sions (see [][]\T1/fi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ). 
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[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
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[][][]\T1/fi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
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[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
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\T1/ptm/m/n/10 Kains \T1/fi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/fi4/m/n/10 <markus.schroeder@ucdconnect.ie>  
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 []  \T1/fi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[] 
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[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
omics Con-sor-tium us-ing Affymetrix hgu133plus2
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[][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
[]$http : / / www . nicebread . de / blog / files / fc02e1635792cb0f2b3cbd1f7e6
c580b-[]10 .
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
 and probes in columns,

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[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
 named "En-trez-Gene.ID",
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bl_gene_id", "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[] 


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se = FALSE)[] 

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[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the 
gene ex-pres-sions (see [][]\T1/fi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ). 
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[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
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[][][]\T1/fi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
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[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
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\T1/ptm/m/n/10 Kains \T1/fi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/fi4/m/n/10 <markus.schroeder@ucdconnect.ie>  
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 []  \T1/fi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[] 
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[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
omics Con-sor-tium us-ing Affymetrix hgu133plus2
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e-sis, must be one of "two.sided"

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[][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
[]$http : / / www . nicebread . de / blog / files / fc02e1635792cb0f2b3cbd1f7e6
c580b-[]10 .
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
 and probes in columns,

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[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
 named "En-trez-Gene.ID",
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bl_gene_id", "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[] 


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se = FALSE)[] 

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[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the 
gene ex-pres-sions (see [][]\T1/fi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ). 
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[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
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[][][]\T1/fi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
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[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
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\T1/ptm/m/n/10 Kains \T1/fi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/fi4/m/n/10 <markus.schroeder@ucdconnect.ie>  
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 []  \T1/fi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[] 
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[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
omics Con-sor-tium us-ing Affymetrix hgu133plus2
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 []\T1/fi4/m/n/10 fuzzy.ttest(x, w1, w2, alternative=c("two.sided", "less", "gr
eater"), check.w = TRUE, na.rm = FALSE)[] 

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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"

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[][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
[]$http : / / www . nicebread . de / blog / files / fc02e1635792cb0f2b3cbd1f7e6
c580b-[]10 .
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 []\T1/fi4/m/n/9 randst <- apply(rands, 1, function(x, xx, ww1, ww2) { return(f
uzzy.ttest(x=xx, w1=ww1[x], w2=ww2[x])[2]) }, xx=xx, ww1=ww1, ww2=ww2)[] 
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
 11\T1/ptm/m/n/10 (2):R18 
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= "EntrezGene.ID", mapping, verbose = FALSE)[] 

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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
 and probes in columns,

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[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
 named "En-trez-Gene.ID",
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 []\T1/fi4/m/n/10 ovcAngiogenic(data, annot, hgs, gmap = c("entrezgene", "ensem
bl_gene_id", "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[] 


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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE 
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 []\T1/fi4/m/n/9 ovcAngiogenic.nkis <- ovcAngiogenic(data=data.nkis, annot=anno
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ene_id", "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[] 

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gmap="entrezgene", do.mapping=TRUE)[] 
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se = FALSE)[] 

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[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the 
gene ex-pres-sions (see [][]\T1/fi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ). 
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[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][] 
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
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[][][]\T1/fi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
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[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
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