GlobalAncova

Calculates a global test for differential gene expression between groups

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("GlobalAncova")

To cite this package in a publication, start R and enter:

    citation("GlobalAncova")

Documentation

PDF R Script GlobalAncova.pdf
PDF R Script GlobalAncovaDecomp.pdf
PDF   Reference Manual

Details

biocViews DifferentialExpression, Microarray, OneChannel, Pathways, Software
Version 3.33.0
In Bioconductor since BioC 1.7 (R-2.2)
License GPL (>= 2)
Depends methods, corpcor, globaltest
Imports annotate, AnnotationDbi
Suggests Biobase, annotate, GO.db, KEGG.db, golubEsets, hu6800.db, vsn, GSEABase, Rgraphviz
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source GlobalAncova_3.33.0.tar.gz
Windows Binary GlobalAncova_3.33.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GlobalAncova_3.33.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center