I have run GAGE to find out the enriched GO and KEGG term between control and chemical treatment for non-model species. In some comparison, some enrichment terms/pathways contained some common genes, then I tried to use "esset.grp" to extract the non-redundant pathways.
However, I am not quite understand how "esset.grp" work and what statistics are used? why th pathway selected in value of essentialSets is non-redundant, but or other? How the argument pc is calculated and why 10e-10?
Please kindly explain more, as I don't have good bioinformatics background and no one in my lab has experience in NGS work.