[BioC] GeneSetCollection from GSEA

Paul Christoph Schröder pschrode at alumni.unav.es
Wed Feb 27 09:21:59 CET 2008

Hello all,

I'm using the GSEABase package For gene set enrichment I used the java software provided by the Broad Institute, but now since I want to use R I'm trying to implement it to my workflow.

If I'm interested only in a gene set collection like 'c2' from MSIGDB, what would be the appropiate command for getting the gene set collection?

I tried:
getBroadSets('msigdb_v2.1.xml', base="http://www.broad.mit.edu/gsea/donwloads.jsp")

But it fails:
Error: 'getBroadSets' failed to create gene sets:
msigdb_v2.1.xml  does not seem to be XML, nor to identify a file name

Thanks a lot!

Paul C. Schröder
Division of Proteomics, Genomics & Bioinformatics
Center for Applied Medicine (CIMA)
University of Navarra
Avda. Pio XII, 55
E-31008 Pamplona, Spain

Tel: +34 948 194700, ext 5023
email: pschrode at alumni.unav.es

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