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Tutorial:selecting result from deseq2

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Nas 1989 • 0

@nas-1989-23201

Last seen 4.0 years ago

south africa/ cape town

Hi I have run differential expression analysis in cancer RNA-seq data vs Normal the data was from TCGA I manage to get result file.

I set the logfold change 2 and alpha 0.001

what I expect to see less number of genes down and up regulated my question what is the best way to downstream or selecting final result ??

Thanks in advance Nasr

deseq2 Tutorial • 1.9k views

ADD COMMENT • link updated 4.1 years ago by Michael Love 41k • written 4.1 years ago by Nas 1989 • 0

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If you post over at biostars.org (which you are welcome to do) please be sure to add more details and all relevant command lines. Currently it is difficult to advise you since from what you write it is unclear what you are actually doing.

ADD REPLY • link 4.1 years ago ATpoint ★ 4.0k

score 1 · Answer 1 · 2020-03-29

As the maintainer of DESeq2, I don't have any specific advice for you here. I usually answer specific questions that are about software usage. This is a more general question about expectations or parameter settings.

Aside from reading the vignette or workflow, you might try posting with a specific question to biostars, if you don't have a specific software usage question.