Hi all,

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.

So which set of pathways should I actually use as my result? The ones found using the adjusted p-value or the one without?

I am still confused about this p-value thing and the difference between the web Reactome and your ReactomePA package. What is the difference in the method of p-value calculation in the web Reactome and your package? I read somewhere that the p-value in Reactome is calculated using the BH method, but why does the p-values differ with the ones from ReactomePA even when I use the similar pvalueAdjustMethod?

Sorry but I am quite new to this type of analysis. I read up on p-value adjustment but still have some difficulty understanding it. Could you please explain all my queries in a simple manner?

Thank you very much.