Entering edit mode
6.1 years ago
chrisgr
▴
20
I have a differentially expressed gene list made with Limma. I can put just the genenames in Enrichr:
http://amp.pharm.mssm.edu/Enrichr/
But I can also add "levels of membership" / "Gene weight" which is number per gene ranging from 0 to 1. Which sounds very nice. But how do I get those numbers? I do have logFC and P.values of each gene but they ofcourse have a bigger range not a number between 0 and 1. So how do I calculate that "gene weight" here?
And why can't I find any further explanations anywhere?
I hope someone knows, thanks!
Did you read the background info? http://amp.pharm.mssm.edu/Enrichr/help#background
I quote:
So their advice is to use crisp set if you don't understand how fuzzy works.
You can read more about the fuzzy implementation in their NAR paper: https://academic.oup.com/nar/article/44/W1/W90/2499357
Because you are probably searching for the wrong terms: in the paper and documentations, the terms crisp gene set and fuzzy gene set are used. Further explanations from Enrichr Online Help:
The paper has this to say about fuzzy gene set analysis: