Hello,

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))) > [1] 3.222392 > > mean(c(2,3,4)) > [1] 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?

Regards,

Dr. Philip de Groot

Wageningen University