[BioC] A question about the gage package

He, Yiwen (NIH/CIT) [C] heyiwen at mail.nih.gov
Mon Mar 25 18:49:27 CET 2013


I am looking into using the gage package for gene set analysis. I would like to test run it on the human diabetic muscle microarray data used in the initial description of GSEA paper. I downloaded the expression data (Diabetes_hgu133a.gct) from the Broad institute website, and also downloaded the C2 gene set there (c2.symbols.gmt). However, the IDs in the expression dataset are Affymetrix probe IDs, while the IDs in the gene set are gene symbols (or Entrez gene IDs if I download another version.)

Your manual says these two IDs should match, and I understand that. But what should I do when they don't match? The examples given in the manual have everything setup the right way already.

I'm using R version 2.15.2 and gage_2.8.0 on Platform: i386-w64-mingw32/i386 (32-bit).

Thank you very much!

Yiwen He 

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