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.