I am working on pathway analysis using GAGE and Pathview. I can determine up-regulated and down-regulated pathways and get corresponding heatmaps, but I have a question on the "type" of counts I should be using. When I did differential gene expression analysis I generated a DGElist that has pseudo.counts which if I understand correctly are transformed and normalized. I also have a Counts Per Million list that was generated after quality filtering of raw counts. I get similar differentially regulated pathways while using either counts but I do not know which one is more appropriate to use. If anyone can help me I would very much appreciate the help. Thanks!
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