I am using Reactome for GO / Pathway Enrichment analysis for my set of DE genes. Besides the web interface, I am also using the ReactomePA R package for the analysis. I am confused with the settings & p-values for these 2.
1) In the Reactome web interface, the results show an entities p-value - is this p-value adjusted or not?
2) Should I use the p-value or adjusted p-value to check my DE genes? When I analyze it in ReactomePA by adjusting the pAdjustMethod, I got different results for none adjusted and bonferonni adjusted.
Could someone please advise?
Thank you very much.