To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("GlobalAncova")
In most cases, you don't need to download the package archive at all.
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Bioconductor version: Release (3.3)
We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany.
Author: U. Mansmann, R. Meister, M. Hummel, R. Scheufele, with contributions from S. Knueppel
Maintainer: Manuela Hummel <m.hummel at dkfz.de>
Citation (from within R,
enter citation("GlobalAncova")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("GlobalAncova")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GlobalAncova")
R Script | GlobalAncova.pdf | |
R Script | GlobalAncovaDecomp.pdf | |
Reference Manual |
biocViews | DifferentialExpression, Microarray, OneChannel, Pathways, Software |
Version | 3.40.0 |
In Bioconductor since | BioC 1.7 (R-2.2) (11 years) |
License | GPL (>= 2) |
Depends | methods, corpcor, globaltest |
Imports | annotate, AnnotationDbi |
LinkingTo | |
Suggests | Biobase, annotate, GO.db, KEGG.db, golubEsets, hu6800.db, vsn, GSEABase, Rgraphviz |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Package Source | GlobalAncova_3.40.0.tar.gz |
Windows Binary | GlobalAncova_3.40.0.zip (32- & 64-bit) |
Mac OS X 10.9 (Mavericks) | GlobalAncova_3.40.0.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/GlobalAncova/tree/release-3.3 |
Package Short Url | http://bioconductor.org/packages/GlobalAncova/ |
Package Downloads Report | Download Stats |
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