Question: Preranked GSEA statistics
1
gravatar for elb
19 months ago by
elb200
Torino
elb200 wrote:

Hi guys, I have a general question regarding the pre-ranked GSEA. I have a list of genes ranked according to the LogFC and then a list of genes that is my geneset. I would like to see if the genes of the geneset are enriched in my ranked list. To do this, I'm running the pre-ranked GSEA. I'm not sure the meaning of NES and FDR. Which is the statistical score to consider to evaluate the enrichment?

Thank you in advance

gsea • 698 views
ADD COMMENTlink modified 19 months ago by alserg630 • written 19 months ago by elb200
1
gravatar for alserg
19 months ago by
alserg630
alserg630 wrote:

NES stands for normalized enrichment score. It's calculated as the enrichment score value of the pathway divided by the average enrichment score of random gene sets of the same size and the same ES sign.

FDR corrseponds to p-value adjusted to multiple hypothesis comparison. Although, if you use the Broad version, it's not a proper adjustment, so be cautious when using it.

ADD COMMENTlink written 19 months ago by alserg630
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