A gene set analysis function for one-sided test (OLS) and two-sided test (multivariate analysis of variance). Three multiple comparison procedures, Dunnett, Tukey, and sequential pairwise comparison, are implemented. MAVTgsa computes the p-values and FDR (false discovery rate) q-values for all gene sets. The p-values for individual genes in a significant gene set are also listed. MAVTgsa generates a GST-plot of the empirical distribution function of the ranked test statistics of a given gene set.
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Chen,J.J. et al. (2007) Significance analysis of group of genes in expression profiling studies, Bioinformatics, 23, 2104.
Tsai,C.A. et al. (2009) Multivariate analysis of variance test for gene set analysis. Bioinformatics, 25, 897.
Documentation reproduced from package MAVTgsa, version 1.2. License: GPL-2