about using TPM with ssGSEA

[白澤昌之]

Hello,

I'm trying to analyze ssGSEA, which is better to use TPM data or log2 (TPM + 1) data?

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Masayuki Shirasawa MD

Division of Genome Biology

National Cancer Center Research Institute

Department of Thoracic Oncology 

National Cancer Center Hospital 

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[Anthony Castanza]

Hello,

 

This is not a scenario we've investigated in detail. Historically we've used untransformed TPM, and for other GSEA-family algorithms, we've not generally recommended log transformation, however, without extensive testing I can't give you a firm answer on what to do here.

 

Using the non-transformed TPM would probably be most in-line with other workflows that use ssGSEA, but depending on what you're trying to do with the results, it could be definitely worthwhile to run ssGSEA with both versions and do some comparisons. If you do so, we'd definitely be interested in hearing about your results.

 

Sorry I couldn't be of more help here,

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

http://gsea-msigdb.org/

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[白澤昌之]

Dear Anthony,

Thanks a lot for your answer! I'm going to try both patterns.

Masayuki Shirasawa 

2022年1月7日金曜日 6:33:23 UTC+9 Anthony Castanza: