Input data

[Hamed Khedmatgozar]

Dear GSEA help group,

I'd like to use the GSEA to see the enrichment analysis of my data. 

I want to see what are the best input values that you suggest. Is it better to have rea_count data or normalized data? 

Thank you, 

Hamed 

[Castanza, Anthony]

Hi  Hamed,

 

I’m not sure I’m familiar specifically with rea_count data, and “normalized data” is a bit ambiguous, what specific method were you considering?

Generally the recommendation for RNA-seq is something like TMM or DeSeq2-normalized counts. Not TPM/FPKM/RPKM.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Department of Medicine

University of California, San Diego

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[Hamed Khedmatgozar]

Dear Anthony, 

I used edgeR to normalize my data. So, I have raw_count, read_count, CPM (TMM). So, as you suggested, TMM will be a better option to use, correct? 

Thank you, 

Hamed 

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