Which group is meant by greater oder less in the gage results?
1
0
Entering edit mode
@matmu
Last seen 12 weeks ago
Germany

I am using the Bioconductor package gage in combination with the gene sets from package msigdbr to perform gene set enrichment analysis. The result object (I called it res) of gage() contains the data frames res$greater and res$less containing up or downregulated pathways. Are the gene sets up/downregulated in the experimental group (parameter samp in function gage()) or the control group (parameter ref in function gage())? I am pretty sure the data frames are related to experimental group but a gene set which I suspected to be significant in greater is significant in less.

Thanks for your help.

gage • 187 views
ADD COMMENT
1
Entering edit mode
Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 3 months ago
United States

Gage compare experimental group (samp) to control group (ref). greater means up regulated in experimental group, less means down regulated.

ADD COMMENT

Login before adding your answer.

Traffic: 488 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