[BioC] Basic question about Limma

[Heidi Dvinge]

Hello Guido,

the M-values are indeed the log2 fold change, so log2(R/G) for the red and
green channel. However, after normalisation the R and G intensities are
usually reported on a log2 scale (from 0-16), and since
log2(R/G)=log2(R)-log2(G) that's probably what you see.

HTH
\Heidi

> Dear List I've a very basic question about the  limma output (and I'm
> newbie
> of MA analysis).
> I'm looking some analysis output .Usually in the M column (if I well
> understand ) I should expect to find the log2-fold change of my
> conditions.Instead I find the difference between the normalized
> expressions...
> Some one could suggest to me how to transform these values in log2  fold
> change?
> Thank you very much and sorry for my silly question
>  Guido Leoni
>
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