Question: GSEA top genes vs all platform
gravatar for ra2967
13 months ago by
ra296720 wrote:


I have done an analysis in LIMMA to obtain the differential expressed genes. However, now I have 2 questions when I perform GSEA:

  • Must I order my samples by fold change (first negative and after positive forld change, por example) in a preranked analysis? Is it better to order by p.val? Can I give the list obtained by limma directly in GSEA?

  • GSEA is usually done with the top genes (let's say, the top 50-100 genes) or must I use THE WHOLE platform (all the 30K probes)?

Thanks in advance

ADD COMMENTlink modified 13 months ago by Charles Warden7.2k • written 13 months ago by ra296720

Have a loot at this thread, may be helpful

ADD REPLYlink modified 13 months ago • written 13 months ago by Prakash1.4k

You can also use gene set tests included in the limma package, i.e. CAMERA and ROAST. CAMERA, in particular, is way, way faster than GSEA. Prof. Smyth has made the MSigDB gene sets available in easy to ingest .rda files at his website:

ADD REPLYlink written 13 months ago by glocke01160
gravatar for Charles Warden
13 months ago by
Charles Warden7.2k
Duarte, CA
Charles Warden7.2k wrote:

GSEA is typically performed on the whole platform, without the differential expression step.

However, you are correct that a pre-ranked list is another option.

ADD COMMENTlink written 13 months ago by Charles Warden7.2k
gravatar for Rashedul Islam
13 months ago by
Rashedul Islam310 wrote:

Instead of using pre-ranked with 50-100 genes, you can use entire set. Then check how many genes have core GSEA enrichment and are differentially expressed.

ADD COMMENTlink written 13 months ago by Rashedul Islam310
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