[BioC] GSEA and Broad gene sets

[Hassane, Duane]

The Broad Institute put out a R script, GSEA.R, which works with their gmt files and uses their KS-based enrichment score metric.

http://www.broad.mit.edu/gsea/software/software_index.html

Though, I have not yet specifically tried using specific BioC packages with Broad .gmt files.

Not sure if that's what you're looking for.

Duane Hassane


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of
Brian_Hare at vrtx.com
Sent: Wednesday, December 05, 2007 2:34 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] GSEA and Broad gene sets



 Are there any detailed instructions available (e.g. vignettes) for how to 
do GSEA on 
 the Broad collection of pathways in Bioconductor?  I see bits and peices 
- e.g. GSEAbase, 
 geneSetTest(limma) - but haven't seen it all put together - thanks

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