As part of a larger project I've implemented GSEA in Matlab.  I want to test my code by comparing my output - p-values for KEGG pathways say, with another implementation.  In my implementation the GSEA algorithm starts from a ranked list of gene ids with real valued weights.  So I want to upload the same list to the tool used for comparison.  However, as I look round tools for GSEA most of them seem to start at an earlier point, requiring the original gene data, which would mean that there would be scope for differences in preprocessing to affect the output, whereas I want a pure comparison of the GSEA part.  

What would you say is the simplest way to perform GSEA (not another enrichment algorithm) on a weighted list of entrez-gene ids?  

I'm fine if it involves some coding, but don't want to get bogged down editing large amounts of other people's code to perform what should be a straightforward test to check that my results are comparable with the expected results.


I believe that http://www.broadinstitute.org/cancer/software/genepattern/modules/docs/GSEAPreranked/1 should work for you.