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 the
gage() function is different from the number of genes produced by the
geneData() function, which is the function to use in order to extract the gene IDs assigned to a significantly enriched pathway.
For example, one pathway has 181 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()?