Thank you Heidi and Neel
I'll give you more details about my data:
The experiments are performed with an affymetrix custom 3' array
here is an example for one probeset :
Normalized expression with gcRMA
                                              control       control
control       case          case           case
    219070_s_at 679,15 734,98 777,32 667,32 507,76 645,37
This is the corrisponden row from limma output  for the same probeset
AFFy ID                 EG        Symbol  M                       A
               t                          P.value                    B
219070_s_at 64598        MOSPD3 -124.008563236060 666.759701175327
-2.27688122341071 0.0489596557364987 -4.19921794672031


2010/4/27 Heidi Dvinge <heidi@ebi.ac.uk>

> 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
> >
> >       [[alternative HTML version deleted]]
> >
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> > Search the archives:
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> >
>
>
>


-- 
Guido Leoni
National Research Institute on Food and Nutrition
(I.N.R.A.N.)
via Ardeatina 546
00178 Rome
Italy

tel     + 39 06 51 49 41 (operator)
       + 39 06 51 49 4519 (direct)

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