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Question: A rational way for selecting the number of DEG with significant p-value for GSEA
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gravatar for Shamim Sarhadi
20 months ago by
Shamim Sarhadi20 wrote:

suppose I have 1000 prob-id(output of the limma) with the significant p-value, should all of them be select for GSEA, or there is a rational way of choosing the number of DEG for GSEA?

ADD COMMENTlink modified 20 months ago by Gordon Smyth32k • written 20 months ago by Shamim Sarhadi20
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gravatar for Steve Lianoglou
20 months ago by
Genentech
Steve Lianoglou12k wrote:

The nice thing about some GSEA methods (like camera and roast) is that you don't need to choose a cutoff, but they rather work over the entire spectrum of changes across a comparison specified in your linear model.

Consider reading through the Gene set analysis and the Gene set testing sections in the PH525x biomedical science book

ADD COMMENTlink written 20 months ago by Steve Lianoglou12k
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gravatar for Gordon Smyth
20 months ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

Since you are analyzing a gene list, I assume that you are doing a simple overlap pathway analysis such as that done by the goana() or kegga() functions in limma. (I wouldn't call these methods GSEA, that's a term I prefer to reserve for more complicated things that are analogous to the GSEA software form the Broad Institute.)

The overlap analyses, whereby we count the number of DE genes in each annotated term or pathway, work best when there are lots of DE genes. So having 1000 DE genes is not by any means too many. However, a few thousand DE genes would be on the high side. In that case, I would trim the list down by using treat() with a higher lfc threshold.

ADD COMMENTlink written 20 months ago by Gordon Smyth32k

Thank you, Gordon Smyth

Your explanation was interesting, well I could try with Broad Institute 

software , http://software.broadinstitute.org/gsea/index.jsp

ADD REPLYlink written 20 months ago by Shamim Sarhadi20
1

Or, since you already are using limma, you could try some of the many GSEA methods it provides as I suggested above (camera, roast, romer, ...)

ADD REPLYlink written 20 months ago by Steve Lianoglou12k
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