I tried the EGSEA package and was hoping to find a better way to do the GSEA. The output column Direction under gsa$mylabel$test.results$mycontrast gives values 1,0, -1. I assume that -1 means the gene set/pathway is down-regulated and 1 means it's up-regulated. My problem is that most of the gene sets/pathways in my test study are -1, and thus down-regulated, which is not consistent with the results I got with other programs such as GAGE (which is one test in EGSEA). I read the pre-print and found no clue.
Thanks a lot,