The topic of this email looks easy enough, but I cannot find in the Limma documentation how the (log2) fold changes are actually calculated.
As you probably now, Limma uses log2-scaled input (originating from e.g. RMA). So, if you want to calculate a log2 fold change, it is possible to keep this log2-transformation into account or to discard it. What I mean with this is that the mean of logged values is lower than the mean of
the unlogged values.
Take for example the series: 2, 3, and 4
> log2(mean(c(2^2, 2^3, 2^4))) >  3.222392 > > mean(c(2,3,4)) >  3
To my opinion, the top method, unlog, calculate the mean, and log2-transform again, is the proper way and I do expect that Limma does it the same way. My question is: is this true?
Dr. Philip de Groot