Thanks for reading. I have a RNA-SEQ data set which I have already processed, I now have a list of up and down-regulated genes with p-values, fold changes, and KO numbers (already ran proteins through KEGG) which contains about 850 genes. I want to run this data through Gage/Pathview to look at any metabolic pathway changes which have occurred under my specific treatment. The gage and pathview vignettes are not commented enough for me (an R newbie) to figure out where I can enter the pipeline with my data file. Without adequate programming comments in the manuals I'm currently unable to follow the procedures.
I'd greatly appreciated any help anyone can give.