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mikelove / preNivolumabOnNivolumab

EDA, QC, and DESeq2 / edgeR analysis of 109 RNA-seq samples of immunotherapy treatment
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Method comparison #1

Open chrarnold opened 2 years ago

chrarnold commented 2 years ago

Hi Michael, thanks a lot for this repo, this should be promoted much more, very important... I wonder whether you have some experience or thoughts to share or to add to the vignette regarding the alternative methods for batch removal. You mention a few, how they perform as compared to RUVSeq? Are there papers out there that systematically compare them? Thanks!

mikelove commented 2 years ago

Thanks for the note.

That's a good question, I think some of the SEQC papers did compare RUV and SVA, but that was a while ago and there may be more up to date ones. Maybe post as a question on and tag RUVSeq authors?

chrarnold commented 2 years ago

Thank you, will do so, I can post the link here once I have done that and then resolve the issue.