GSVA: The Gene Set Variation Analysis package for microarray and RNA-seq data

The GSVA package implements a non-parametric unsupervised method, called Gene Set Variation Analysis (GSVA), for assessing gene set enrichment (GSE) in gene expression microarray and RNA-seq data. In contrast to most GSE methods, GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene set by sample matrix. Thereby allowing for the evaluation of pathway enrichment for each sample. This transformation is done without the use of a phenotype, thus facilitating very powerful and open-ended analyses in a now pathway centric manner. In this vignette we illustrate how to use the GSVA package to perform some of these analyses using published microarray and RNA-seq data already pre-processed and stored in the companion experimental data package GSVAdata.