how to create -gct and .cls files from RNASeq counts?

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4.2 years ago

annamariabugaj • 0

This is probably a stupid question but I really can not find an answer... I want to compare two DEGs sets from two different experimental settings in order to create a 'common DEGs set' and I found out that GSEA is a good way to do it but I need two types of files .gct and .cls

How do I create this files using my counts matrix that I was using for DESeq2? I found this https://rdrr.io/bioc/ArrayTools/man/output.cls.html but I am not sure what 'variable of interest' means and how exactly should I use this function (and similarly output.gct().

Or is it ok to just plot the Venn diagram for the two lists of DEGs? I am a bit lost after reading and searching....

gct GSEA cls RNA-Seq DESeq2 • 2.8k views

ADD COMMENT • link updated 13 months ago by Ram 43k • written 4.2 years ago by annamariabugaj • 0

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I think you should read first what GSEA is actually doing. It is not giving you a common set of genes but will tell you if your DEGs will be signifiantly enriched (in either direction, up, down) compared to a set of genes (typically curated sets of genes e.g. from MSigDB).

ADD REPLY • link 4.2 years ago by ATpoint 81k

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