[BioC] calculation of "M" in limma topTable

[Kimpel, Mark William]

I am unsure how to interpret the M-value produced by limma topTable when analyzing a multi-factoral, multi-level experiment.

As an example, suppose I test one gene under the same 2 conditions (1 and 2) in two different experiments (A and B). The mean expressions in the two experiments are very different but in both cases condition 1 has higher expression levels than condition 2. I look at the contrast of condition 1 vs. condition 2 ((A1 + B1) - (A2 + B2)). 

How does topTable calculate M?

Thanks,

Mark W. Kimpel MD	

Department of Psychiatry
Indiana University School of Medicine
Biotechnology, Research, & Training Center
1345 W. 16th Street
Indianapolis, IN  46202