Dear list,
For GAGE package, I converted Affymetrix hg u133 plus 2 probeset IDs to gene names so that both "exprs" and "gsets" use same gene ID system. But when i got the results from Biomart, the data showed different probe IDs corresponding to same gene name. So if i have to replace the probe IDs in "exprs"  to gene names  i will have to enter same gene name for different probe IDs which is unusual as before "exprs" had unique probe set IDs.
How does GAGE encounter this problem? Doesn't this affect the result of the analysis?
Thanks,
Jung

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