GSEA and normalized reads count

Question

[Morris_Chair]

Hello everyone,

I want to make a GSEA using the online tool of the Broad Institute. To do that I generally use FPKM or RPKM matrix and I was wondering if you think it's ok to use the normalized read file that I get as output from DESeq2

thank you

Answer 1

[guillaume.rbt]

If you have already run DEseq2 it would be easier for you to use GSEA with the "preranked" mode, giving as input a metric based on the logFC and the pvalues that you got as result of your differential expression.

It is pretty well explained here : http://crazyhottommy.blogspot.com/2016/08/gene-set-enrichment-analysis-gsea.html