Genearating pre ranked gene list for GSEA

[Manjunatha B K]

I have used Deseq2 for my differential expression analysis and to rank the genes i have used log2FoldChange of all the genes which will fall below the p-value cutoff. I have arranged the genes in the Descending order on the basis of log2FoldChange value and used in GSEA. which method i should prefer, whether fold change * -log10 pvalue or stat column obtained in DeSeq2 or Log2FC alone .

Thank you.

Manjunath

[Castanza, Anthony]

Hi Manjunath

 

You should include all genes, not just those that pass an arbitrary p-value cutoff. GSEA needs the information from the non-significantly differentially expressed genes when scoring the set and set nulls.

As to which metric specifically to use, I would lean towards using either the test statistic (i.e. wald) or the log2FC, but it is our policy not to provide an official recommendation for GSEA Preranked metric selection.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

--
You received this message because you are subscribed to the Google Groups "gsea-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gsea-help+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/7d8b7c53-b73c-4f6e-bcb3-f98efad5723an%40googlegroups.com.