Question: GSEA For Paired Microarray Data
0
gravatar for dompearcejankowski
4.2 years ago by
United Kingdom
dompearcejankowski0 wrote:

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

gsea matched pair paired enrichment • 1.6k views
ADD COMMENTlink modified 3.4 years ago by Gordon Smyth780 • written 4.2 years ago by dompearcejankowski0
0
gravatar for Mo
4.2 years ago by
Mo880
/
Mo880 wrote:

@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 

ADD COMMENTlink written 4.2 years ago by Mo880
0
gravatar for dompearcejankowski
4.2 years ago by
United Kingdom
dompearcejankowski0 wrote:

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?

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by dompearcejankowski0
0
gravatar for Gordon Smyth
3.4 years ago by
Gordon Smyth780
Australia
Gordon Smyth780 wrote:

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).

ADD COMMENTlink written 3.4 years ago by Gordon Smyth780
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