I'm pretty new to Rstudio and I'm doing gene expression analysis using R. After doing the differential expression analysis I would now like to understand which pathways are over and underexpressed. The problem that I have is that I got the Fold Change comparisons between 4 groups, being: WNTvsSHH, WNTvsG3, WNTvsG4, SHHvsG3, SHHvsG4 and G3vsG4. All pathway analysis that I find onlye have the fold change between Treated and Untreated. Can I only do KEGG analysis between 2 groups? Or is there other way that can do this?
Aprecciate your help.