fgsea
1
0
Entering edit mode
7 weeks ago
Mary • 0

Hi all, I have a question that may be obvious. With the package fgsea, that uses a pre-ranked gene list, are the permutations carried out are gene set and not phenotype permutations: is that correct? Thank you!

permutations fgsea • 258 views
ADD COMMENT
2
Entering edit mode
7 weeks ago
LChart 840

The gene list itself is permuted; so the comparison is the input ranking versus random rankings.

A phenotype permutation would be repeating (permute case/control labels --> differential expression --> top table --> fGSEA); and in such a case you could disable the internal fGSEA permutations entirely.

ADD COMMENT

Login before adding your answer.

Traffic: 2195 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6