This page contains the source code to generate enrichment scores from a gene expression matrix. The code in written in R and requires bioconductor.
R file with functions required to compute enrichment: EnrichmentScoreCalc.R
R file with detailed instructions on how to run the enrichment score. In this example you will be able to re-generate the enrichment matrix in the download section: RunEnrichmentCode.R
Note that computing the enrichment matrix is very intensive computationally and requires a machine with at least 16Gb of RAM. The BA1 data set takes at least 10 hours to run on a decent multicore 64-bit machine.