Preranked GSEA statistics

Question

[elb]

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

Answer 1

[alserg]

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.