I used both gage package in R and GSEA software for KEGG pathway analysis and since the 2 tools have different algorithms, I got slightly different results in the list of genesets. I was able to find the genes in each gene set from GSEA from their website, but I don't seem to find the gene list of some gene sets that I got as a result of GAGE analysis on GSEA website. A couple of those are:
hsa04659 Th17 cell differentiation
hsa04380 Osteoclast differentiation
I could not find these pathways in GSEA:C2:CP:KEGG collection. I did find the list of genes on KEGG website(http://www.genome.jp/dbget-bin/www_bget?hsa04659), but I would like to download this list. Does anyone know how to get the list of genes in these genesets? Is there an R packages that allows you to download genes in a geneset from KEGG database?