[BioC] [Limma] M value in contrast test

[James W. MacDonald]

Marcelo Luiz de Laia wrote:
> Hi limma Users,
> 
> I did a contrast in our analisis like this:
> 
> (mutant treated-mutant control)-(wildtype treated-wildtype control)
> 
> We are interested in to known what "M" value means in this situation?

This contrast gives you those genes significant in the interaction. In 
other words, you are looking for genes that respond differently to 
treatment in the wild type samples as compared to the mutant. Therefore, 
the M value quantifies the fold change of the different responses.

For instance, if gene x in the mutant sample is unaffected by treatment 
and the same gene in wildtype is downregulated two fold, the M value 
will be about 1 indicating that there is a two-fold difference in the 
response to treatment in the two groups.

Does that help?

Jim


> 
> In limma users guide there are two interpretation for "M" value: fold 
> change or intensities.
> 
> Thanks in advanced
> 
> Marcelo
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
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