[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"
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]))
 4.7944159 0.2087391 -1.2756344
But when I made the conversion with MA.RG(RG) (I need that for following
>RGMA <- MA.RG(RG)
 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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