Which group is meant by greater oder less in the gage results?
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@matmu
Last seen 26 days 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.

gage • 365 views
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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 4 weeks ago
United States

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