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

 


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