Dear list, I have expression data with Affymetrix hg u133 plus 2 probeset IDs & gene set data with gene names. So both gene set and expression data are not using the same gene ID system which is a requirement to run the GAGE analysis. So the problem is that if i convert the Probeset IDs to gene name, i get a single gene name for multiple probes. So the expression data will now have multiple rows with same gene name. IS THIS VALID IN GAGE? How the GAGE package tackles this problem? & If i want to convert the gene names in gene set to Affymetrix hg u133 plus 2 probeset IDs then the problem is WHICH probeset ID should i choose if multiple probeset IDs are associated with that gene. Thanks, Jung [[alternative HTML version deleted]]

Dear list, I have expression data with Affymetrix hg u133 plus 2 probeset IDs & gene set data with gene names. So both gene set and expression data are not using the same gene ID system. Both gene set and expression data should use the same GENE ID system which is a requirement of the GAGE analysis. So the problem is that if i convert the Probeset IDs to gene name, i get a single gene name for multiple probes. So the expression data will now have multiple rows with same gene name. IS THIS VALID IN GAGE? How the GAGE package tackles this problem? GSEA can address this problem but how GAGE does it & If i convert the gene names in gene set to Affymetrix hg u133 plus 2 probeset IDs then the problem is WHICH probeset ID should i choose if multiple probeset IDs are associated with that gene. Thanks, Jung [[alternative HTML version deleted]]