# GlobalAncova v3.36.0

## 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.

## Functions in GlobalAncova

 Name Description 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 No Results!