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

Giulio Di Giovanni perimessaggini at hotmail.com
Fri Apr 1 18:06:34 CEST 2005

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

An object of class "RGList"
[1,]  407
[2,] 4304
[3,]  531

[1,]  291
[2,] 3571
[3,]  394

[1,]  518
[2,]  518
[3,]  493

[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]))
[1]  4.7944159  0.2087391 -1.2756344

But when I made the conversion with MA.RG(RG) (I need that for following 
I obtain:

[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,


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