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

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
Date of publicationNone
MaintainerManuela Hummel <m.hummel@dkfz.de>
LicenseGPL (>= 2)
Version3.42.0

View on Bioconductor

Functions

colon.normal Man page
colon.pheno Man page
colon.tumour Man page
GABroad Man page
GAGO Man page
GAKEGG Man page
GlobalAncova Man page
GlobalAncova.closed Man page
GlobalAncova.closed,matrix,list,formula,formula,ANY,missing,miss Man page
GlobalAncova.closed,matrix,list,formula,missing,ANY,missing,miss Man page
GlobalAncova.closed,matrix,list,missing,missing,missing,ANY,ANY, Man page
GlobalAncova.closed-methods Man page
GlobalAncova.decomp Man page
GlobalAncova,matrix,formula,formula,ANY,missing,missing,missing- Man page
GlobalAncova,matrix,formula,missing,ANY,missing,missing,characte Man page
GlobalAncova,matrix,missing,missing,missing,ANY,ANY,missing-meth Man page
GlobalAncova-methods Man page
pair.compare Man page
pathways Man page
phenodata Man page
Plot.all Man page
Plot.genes Man page
Plot.genes,matrix,formula,formula,ANY,missing,missing,missing-me Man page
Plot.genes,matrix,formula,missing,ANY,missing,missing,character- Man page
Plot.genes,matrix,missing,missing,missing,ANY,ANY,missing-method Man page
Plot.genes-methods Man page
Plot.sequential Man page
Plot.subjects Man page
Plot.subjects,matrix,formula,formula,ANY,missing,missing,missing Man page
Plot.subjects,matrix,formula,missing,ANY,missing,missing,charact Man page
Plot.subjects,matrix,missing,missing,missing,ANY,ANY,missing-met Man page
Plot.subjects-methods Man page
vantVeer Man page

Files

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

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

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

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