I am trying to use edgeR for differential expression analysis. I have 3 replicates for WT and 3 replicates for MUT. I run edgeR with the condition WT-MUT and it gives me the logCPM and logFC values in the output file.
It also outputs a normalized counts file.
How are the logCPM and logFC values calculated for a comparison between 2 conditions, and how can I calculate them manually from the normalized counts file? Do I have to take the average of the 3 WT replicates and average of the 3 MUT triplicates and then subtract the 2 averages to get logCPM? and how about logFC then?