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GlobalAncova (version 3.36.0)

Calculates a global test for differential gene expression between groups

Description

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.

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Version

Version

3.36.0

License

GPL (>= 2)

Maintainer

Manuela Hummel

Last Published

February 15th, 2017

Functions in GlobalAncova (3.36.0)

Plot.subjects

Subjects Plot for GlobalAncova
vantVeer

Gene expression data
colon.normal

Gene expression data
Plot.sequential

Visualization of sequential decomposition
colon.pheno

Covariate information for the colon data
Plot.subjects-methods

Methods for Function Plot.subjects
GlobalAncova-methods

Methods for Function GlobalAncova
GlobalAncova.closed-methods

Methods for Function GlobalAncova.closed
colon.tumour

Gene expression data
GlobalAncova

Global test for differential gene expression
GlobalAncova.closed

Closed testing procedure for testing several groups of genes using GlobalAncova
GlobalAncova gene set testing methods

Gene set testing of gene set databases using GlobalAncova
phenodata

Covariate information for the van t'Veer data
Plot.all

Combined visualization of sequential decomposition and influence of single genes on the GlobalAncova statistic
pathways

Cancer related pathways
pair.compare

Pairwise comparisons of factor levels within GlobalAncova
Plot.genes-methods

Methods for Function Plot.genes
Plot.genes

Genes Plot for Global Ancova