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Question: GSEA threshold question
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gravatar for bhgyu
5 months ago by
bhgyu20
bhgyu20 wrote:

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!

ADD COMMENTlink written 5 months ago by bhgyu20

any reproducible example?

ADD REPLYlink written 5 months ago by Guangchuang Yu800
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