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GSEA and normalized reads count

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

rna-seq deseq2 gsea
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written by Morris_Chair Morris_Chair

1 answer

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

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written by guillaume.rbt guillaume.rbt

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