Hi Yiwen, Jim?s suggestion would work well. The gage package now has a secondary vignette about data preparation on gene set or pathway analysis. It covers: gene set and expression data input, probe set ID, transcript and gene ID conversion. You can find some examples on how to do Probe set ID or gene ID conversion in Section 4-5. Notice that you need to update to the latest version of gage: http://bioconductor.org/packages/2.12/bioc/html/gage.html. And you also need to install the latest gageData package. Hope this addresses your problem. Thanks! Weijun On 3/25/2013 1:49 PM, He, Yiwen (NIH/CIT) [C] wrote: >Hi, >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 >DCB/CIT/NIH/HHS