edgeR differential expression for replicates calculation


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?


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Hi @awezm1

The tool as wrapped for Galaxy is the same as the line-command version.

Bioconductor documents the algorithm at their website here in the linked publication: Bioconductor - edgeR

There is also some Q&A about the functions. The short answer is that the calculations involve more variables than those you list out. Example: Calculation of logFC in edgeR