Question: GAGE or GSEABase using expression data and pathway.gmt file for mouse
gravatar for snishtala03
10 months ago by
snishtala030 wrote:


I have mouse data for 8 samples (2 conditions, 4 samples each). I performed RNA-Seq analysis and have expression data for different genes across these 8 samples. I also downloaded pathway file from

I am trying to do gene set enrichment analysis using R packages GSEABase or GAGE but the tutorial is not being very helpful for this case. moreover, since it is mouse data, I am not sure if I can use the R package to do this.

Please let me know your suggestions.


ADD COMMENTlink modified 10 months ago by Luo Weijun1.4k • written 10 months ago by snishtala030
gravatar for Luo Weijun
10 months ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:

gage package has a tutorial for data preparation, which described how to use gmt file as gene set data:

gage can definitely be used for mouse data, please follow the main tutorial:

for more info about gage function, in R do:



since you gene set data use gene symbols, make sure you RNA-seq or expression data use gene symbols too.


You may also follow the RNA-seq pathway analysis workflow:


ADD COMMENTlink written 10 months ago by Luo Weijun1.4k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 458 users visited in the last hour