GSEA For Paired Microarray Data

Question

[dompearcejankowski]

Hi,

I'd like to carry out a gene set enrichment analysis using paired samples (before and after treatment samples from the same patient) but I'm having trouble finding any method, software or R package to accomplish this.

Can anyone highlight the best way to go about this analysis?

Much appreciated,

Dominic

Answer 1

[Mo]

@dompearcejankowski do you know why no body replied your question? I think because you did not search enough. simply go to the google and write for example "Biostar GSEA" you will find 100 messages. if none helps, then simply google it without Biostar, which I believe you will find 1000 pages explaining gene set enrichment analysis and how to deal with it. I used to write here when I faced any simple problem like you but what I do now, I first search and if I face any SPECIFIC problem then I write here to get opinion of people.

Hope this helps you get running your project

[dompearcejankowski]

Hi Mo,

Thanks for your reply, though I believe my question still stands.

That question is - is there a method for GSEA that takes into account paired/matched data?

That question is not - how do I perform GSEA?

Google is woefully unhelpful on this occasion

Ostensibly I believe I'm asking a similar question to the one listed here: Pathway Analysis For Paired Microarray Data & Paired Rna-Seq Data?

Answer 2

[Gordon Smyth]

The limma package analyses paired experiments for both microarrays and RNA-seq, and has quite a few options for pathway analysis of the results (GO, KEGG, MSigDB etc).