I am using the Bioconductor package gage in combination with the gene sets from package msigdbr to perform gene set enrichment analysis. The result object (I called it res) of gage() contains the data frames res$greater and res$less containing up or downregulated pathways. Are the gene sets up/downregulated in the experimental group (parameter samp in function gage()) or the control group (parameter ref in function gage())? I am pretty sure the data frames are related to experimental group but a gene set which I suspected to be significant in greater is significant in less.

Thanks for your help.

Gage compare experimental group (samp) to control group (ref). greater means up regulated in experimental group, less means down regulated.