GSEA threshold question
0
0
Entering edit mode
bhgyu ▴ 30
@bhgyu-13069
Last seen 3.3 years ago

Hi guys,

Would someone have an explanation for the following? 

I've run multiple meta analysis and successfully did ORA at p < 0.05

However, whenever I try doing GSEA (using ReactomePA or clusterProfiler) it fails at p < 0.05 and only works at p < 1 (I'm using the Fisher's p val ranked genes).

If I run GSEA within the individual data sets (not meta analysed) it works fine at 0.05.

The above issue is the case for a total of 6 meta analysis which seriously makes me doubt whether that should be the case...

Any suggestions how I can run GSEA on meta analysed genes or justify the p < 1 threshold? 

Much appreciated. Cheers!

GSEa r clusterprofiler reactomepa • 760 views
ADD COMMENT
0
Entering edit mode

any reproducible example?

ADD REPLY

Login before adding your answer.

Traffic: 429 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6