GAGE or GSEABase using expression data and pathway.gmt file for mouse
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@snishtala03-12950
Last seen 4.4 years ago

Hello,

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 http://download.baderlab.org/EM_Genesets/April_01_2017/Mouse/symbol/Mouse_AllPathways_April_01_2017_symbol.gmt

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.

Thanks!

R GSEA GAGE pathways • 1.1k views
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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 10 weeks ago
United States

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

http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/dataPrep.pdf

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

http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/gage.pdf

for more info about gage function, in R do:

?gage

 

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:

http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf

 

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