GlobalAncova: Calculates a global test for differential gene expression between groups
Version 3.44.0

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.

AuthorU. Mansmann, R. Meister, M. Hummel, R. Scheufele, with contributions from S. Knueppel
Bioconductor views DifferentialExpression Microarray OneChannel Pathways
Date of publicationNone
MaintainerManuela Hummel <m.hummel@dkfz.de>
LicenseGPL (>= 2)
Version3.44.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GlobalAncova")

Popular man pages

GlobalAncova: Global test for differential gene expression
GlobalAncova.closed: Closed testing procedure for testing several groups of genes...
GlobalAncova.decomp: GlobalAncova with sequential and type III sum of squares...
GlobalAncova-methods: Methods for Function GlobalAncova
phenodata: Covariate information for the van t'Veer data
Plot.genes: Genes Plot for Global Ancova
vantVeer: Gene expression data
See all...

All man pages Function index File listing

Man pages

colon.normal: Gene expression data
colon.pheno: Covariate information for the colon data
colon.tumour: Gene expression data
genesettesting: Gene set testing of gene set databases using GlobalAncova
GlobalAncova: Global test for differential gene expression
GlobalAncova.closed: Closed testing procedure for testing several groups of genes...
GlobalAncova.closed-methods: Methods for Function GlobalAncova.closed
GlobalAncova.decomp: GlobalAncova with sequential and type III sum of squares...
GlobalAncova-methods: Methods for Function GlobalAncova
pair.compare: Pairwise comparisons of factor levels within GlobalAncova
pathways: Cancer related pathways
phenodata: Covariate information for the van t'Veer data
Plot.all: Combined visualization of sequential decomposition and...
Plot.genes: Genes Plot for Global Ancova
Plot.genes-methods: Methods for Function Plot.genes
Plot.sequential: Visualization of sequential decomposition
Plot.subjects: Subjects Plot for GlobalAncova
Plot.subjects-methods: Methods for Function Plot.subjects
vantVeer: Gene expression data

Functions

Files

DESCRIPTION
NAMESPACE
R
R/GlobalAncova.R
R/GlobalAncova.closed.R
R/GlobalAncova.decomp.R
R/Plot.all.R
R/Plot.genes.R
R/Plot.sequential.R
R/Plot.subjects.R
R/approximation.R
R/genesettesting.R
R/pair.compare.R
R/permutation.R
R/zzz.r
build
build/vignette.rds
data
data/colon.normal.rda
data/colon.pheno.rda
data/colon.tumour.rda
data/pathways.rda
data/phenodata.rda
data/vantVeer.rda
inst
inst/doc
inst/doc/GlobalAncova.R
inst/doc/GlobalAncova.pdf
inst/doc/GlobalAncova.rnw
inst/doc/GlobalAncovaDecomp.R
inst/doc/GlobalAncovaDecomp.pdf
inst/doc/GlobalAncovaDecomp.rnw
man
man/GlobalAncova-methods.Rd
man/GlobalAncova.Rd
man/GlobalAncova.closed-methods.Rd
man/GlobalAncova.closed.Rd
man/GlobalAncova.decomp.Rd
man/Plot.all.Rd
man/Plot.genes-methods.Rd
man/Plot.genes.Rd
man/Plot.sequential.Rd
man/Plot.subjects-methods.Rd
man/Plot.subjects.Rd
man/colon.normal.Rd
man/colon.pheno.Rd
man/colon.tumour.Rd
man/genesettesting.Rd
man/pair.compare.Rd
man/pathways.Rd
man/phenodata.Rd
man/vantVeer.Rd
src
src/GlobalAncova.c
src/GlobalAncova.h
src/ludcmp.c
src/ludcmp.h
src/matrix.c
src/matrix.h
vignettes
vignettes/GlobalAncova.rnw
vignettes/GlobalAncovaDecomp.rnw
vignettes/references.bib
GlobalAncova documentation built on May 20, 2017, 9:20 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.