Since I am working on non model species green mussel and intertidal whelk, I would like to know can I use GAGE to perform gene set analysis for control and chemical treatment groups (n=2 / n=3)? If yes, how can I do it?
I have done de novo transcriptome and worked out the KEGG (Ko and K number without specific species) and GO (GO number without specific species). Is that possible to customize my own gene annotation file and perform available analysis in GAGE?
Can anyone help me about that? I have read the GAGE and pathview doc, but I cannot figure out the way to do so. I am running out of time to finish my MPhil study ><".