Why t-test for differential gene expression?

[Joshua Stephen]

Hi,

I am wondering why cbioportal uses a simple t-test to get the DEGs between any given custom patient groups, and why not more sophisticated parametric tests (like deseq2) or the more preferable non-parametric tests like Wilcoxon-rank sum test which has been shown to perform best recently. Please help me understand how the t-test is robust/sufficient here. Thank you for your time!

Joshua  

[de Bruijn, Ino]

Thanks for reaching out, Joshua!

 

I think those are all good ideas for an enhancement of the DEG we currently offer. I filed a ticket:

 

https://github.com/cBioPortal/cbioportal/issues/10915

 

Best wishes,

Ino

 

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