[BioC] Strange signal Log-Ratios with MA.RG

[Wolfgang Huber]

Ciao Giulio,

this is a commonly known limitation of log-ratios. It appears that your 
problem is that MA.RG(RG) does not calculate

    log2((RG$R-RG$Rb)/(RG$G-RG$Gb))

but rather

    log2(RG$R-RG$Rb) - log2(RG$G-RG$Gb)

and these are different when the individual differences are non-positive 
but the quotient in the first expression is not.

Now some advertisement... For "generalized log-ratios" that avoid this 
problem, coincide with the usual log-ratio when the latter is 
well-defined, and are biologically and statistically meaningful 
shrinkage estimators otherwise, see the "vsn" package and accompanying 
paper(s). Shrinkage estimators sacrifice a small bias for a significant 
reduction in variance, so that the MSE decreases. "vsn" is one of the 
choices for "method" in normalizeBetweenArrays {limma}.

  Cheers
    Wolfgang


-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber
-------------------------------------


Giulio Di Giovanni wrote:
> Hi to all,
> 
> I have a problem that really I cannot solve.
> 
> Some signal log-ratios given to me converting a RGlist with MA.RG(RG) 
> are different from the ones calculated directly, that's the point:
> 
> Looking some .gpr files, I build a RGList with
> 
> RG <- read.maimages(source="genepix", ext="gpr)
> 
> and I obtain for the first 3 genes and the first sample the following 
> Red and Green Foreground and Background intensities
> 
> RG[1:3,1]
> An object of class "RGList"
> $R
>     63MG
> [1,]  407
> [2,] 4304
> [3,]  531
> 
> $G
>     63MG
> [1,]  291
> [2,] 3571
> [3,]  394
> 
> $Rb
>     63MG
> [1,]  518
> [2,]  518
> [3,]  493
> 
> $Gb
>     63MG
> [1,]  295
> [2,]  295
> [3,]  302
> 
> That's to say that log ratios are:
> 
>> za <- log2((RG$R[1:3]-RG$Rb[1:3])/(RG$G[1:3]-RG$Gb[1:3]))
>> za
> 
> [1]  4.7944159  0.2087391 -1.2756344
> 
> But when I made the conversion with MA.RG(RG) (I need that for following 
> analysis)
> I obtain:
> 
>> RGMA <- MA.RG(RG)
>> RGMA$M[1:3,1]
> 
> [1]         NA  0.2087391 -1.2756344
> 
> And this happens for several other genes and samples. Most values are 
> exactly equal, others have NAs ...
> 
> Please, there's someone who could say what I'm doing wrong ?  There's 
> some limitations or some filtering I'm not noticing.. ?
> 
> Thanks in advance,
> 
> Giulio
> 
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