Discrepancy in gene set size between gage() and geneData()

Question

[serpalma.v]

Dear community,

I have run GAGE and Pathview on my microarray data. Everything worked fine.

However, the number of genes assigned to a kegg pathway after using thegage() function is different from the number of genes produced by thegeneData() function, which is the function to use in order to extract the gene IDs assigned to a significantly enriched pathway.

For example, one pathway has181 genes in the variable set.size after using gage(), but when that pathway is used in geneData() with the whole expression set, it returns 196. I tried two more pathways and similar results appeared 34 vs 37 and 15 vs 17.

How can I know exactly which are the genes that are contained in the variable set.size after using gage()?

Many thanks!