Significance of P value in GSEA

Question

[Pumla]

I am having a hard time understanding the biology behind the significance of p-value in calculating ranked gene list when doing gene sset enrichment analysis, because based on what i observe we multiply the fold change and p value to get ranked list of genesm but what significance does the p value mean.

Answer 1

[dthorbur]

You've just stumbled into an ongoing and sometimes heated debate between 2 main factions of statisticians. Here is a pretty good review about the subject on the relevance of p-values in biology.

However, your post doesn't ask any specific questions, so I can't comment other than saying the significance of p-values is contentious.

Answer 2

[jv]

we multiply the fold change and p value to get ranked list

This isn't the only way to rank genes. Personally I use the stat metric from the DESeq2 results for ranking differentially expressed gene results. But there are other ways of ranking. This paper performs a bench mark of different ranking options.