Hello! I am a new user of pathview, and I have a very basic question that I couldn't figure out from reading the manual or the online tutorial. I have RNA-seq data from 2 groups that is log2 transformed. I took the average log2 expression of the experimental group and divided by the average log2 expression of the control group for each gene. When the experimental group is expressed less (let's say a ratio of 0.95), it should be green on the KEGG graph, but whenever I try it the gene actually shows up red. Is this maybe because the scale goes from -1 to 1 (green to red), and 0.95 is close to 1? How can I make genes expressed less in the experimental group actually show up as green? Do I need to further transform the fold change ratio? Or am I going about this completely wrong to begin with? Any suggestions would be very appreciated!
Oops, it was a simple math error. To get the fold change I should have subtracted the log2 expression values, not divided!