pathway analysis on FDR?

[marwa38]

HI guys
It is not an issue it a question regarding enrichmenet analysis.
Do you recommend running pathway analysis without FDR cutt-off so it is independent of DGE genes?

I am a bit new to rnaseq so your comments are helpful.
M

[risserlin]

We recommend pathway analysis on a ranked unthresholded list if possible with your dataset. Please see - https://www.nature.com/articles/s41596-018-0103-9 for the details.