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

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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
Date of publication
None
Maintainer
Manuela Hummel <m.hummel@dkfz.de>
License
GPL (>= 2)
Version
3.42.0

View on Bioconductor

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

Files in this package

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