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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Chih-Yi Chien, Chen-An Tsai, Ching-Wei Chang, and James J. Chen
Maintainer: Chih-Yi Chien <email@example.com>
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.
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