GSEA overexpressed vs. underexpressed genes · Biostar

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GSEA overexpressed vs. underexpressed genes

Hi, I am new to GSEA analysis and I was wondering the common approach for this analysis.

I see some references having GSEA analysis with all genes together (overexpressed and underexpressed genes) but found other references running GSEA separately for overexpressed genes and underexpressed genes after DEseq. What are your opinions/thoughts on this? Which approach is more common? Also, what is the common threshold (p-value and q-value) after running GSEA?

Thanks ahead.

gsea rnaseq

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updated 4.4 years ago by GenoMax

• written 4.4 years ago by BioInfoNewbie •

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