GSEA for RNA seq
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5.6 years ago

Dear all,

I am analyzing a RNA seq data and I've get through DE analysis. Now I want to do GSEA analysis.

What I got:

DESeq2 results. I rank the results in p-value and use the code here to generate rank file. (How to generate a rank file from gene expression data)

When I try to load this rnk file into GSEA and do analysis(Run GSEA on a pre-ranked gene list), I always get a 1001 error, which is this: 1001 error

The rnk file i used is like this:

EPS8L2 1.76163

TINAGL1 1.73341

KLF10 1.73241

AK093534 1.71381

TPGS1 1.70878

...

And I basically choose the parameter follow the instruction here. But I am not so sure about which Gene sets database should I choose in GSEA(I tried c2.cp.kegg.v5.1.symbols.gmt & c2.cp.reactome.v5.1.symbols.gmt). I leave most of the parameter default and change the max size and min size but still get the same error.

Can anyone kindly help me out with that?

Cheers!

RNA-Seq • 4.9k views
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Entering edit mode

What OS are you using? The bash script from that blog post is pretty specific for Ubuntu/Debian type Linuxes and might not work for OSX, Slack, etc. You might want to try an R script to generate the rank file. Also note that the rank file should be tab separated, and the gene names need to match exactly with the gmt file you're using. Also I would start with Reactome as that's a relatively small gene set library that covers the majority of biological pathways and is well maintained.

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