[BioC] simple qc "subscript out of bounds error"

[Fabrice Girardot]

Hi everyone,

I am trying to use the quality controls features of the simpleaffy package for drosophila arrays. I get a subscript out of bounds error message. Is this simply a memory problem ?
Furthermore, I use the ReadAffy function to generate the affybatch rather than the read.affy because this last one doesn't seem to work. My feeling is that read.affy expects to find some unexisting files that are not described in the covdesc table (files ./1, ./2, etc.).

Any help would be greatly appreciated, thanks !


> raw.data2 <- read.affy()
Error in read.affybatch(filenames = filenames, phenoData = phenoData,  : 
        Could not open file ./1
> raw.data <- ReadAffy()
> mas5.data <- call.exprs(raw.data, "mas5")
Background correcting
Retrieving data from AffyBatch...done.
Computing expression calls... 
..................done.
scaling to a TGT of 100 ...Scale factor for: C:/Data/Cs03H1.CEL 1.52888604076715 
Scale factor for: C:/Data/C03H2.CEL 2.94918428845319 
Scale factor for: C:/Data/C03T1.CEL 1.955373320589 
Scale factor for: C:/Data/C03T2.CEL 2.36932486617296 
Scale factor for: C:/Data/C03T3.CEL 2.70407750255314 
Scale factor for: C:/Data/C03W1.CEL 2.04209021063332 
Scale factor for: C:/Data/C03W2.CEL 1.68923246428869 
Scale factor for: C:/Data/C03W3.CEL 1.66919901234788 
Scale factor for: C:/Data/C40H1.CEL 1.96333816670913 
Scale factor for: C:/Data/C40H2.CEL 4.38532511336333 
Scale factor for: C:/Data/C40H3.CEL 0.502132463763216 
Scale factor for: C:/Data/C40T1.CEL 1.66060349786906 
Scale factor for: C:/Data/C40T2.CEL 1.66459847049995 
Scale factor for: C:/Data/C40T3.CEL 1.27538944250907 
Scale factor for: C:/Data/C40W1.CEL 1.28504889307826 
Scale factor for: C:/Data/C40W2.CEL 1.84998547025285 
Scale factor for: C:/Data/C40W3.CEL 0.434921832334024 
Scale factor for: C:/Data/C40W4.CEL 0.822459661709724 
> qc.data <- qc(raw.data, mas5.data)
Getting probe level data...
Computing p-values
Doing PMA Calls
Error in qc.affy(unnormalised, ...) : subscript out of bounds


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Fabrice Girardot, Post-Doctorant
Equipe de Biologie Virtuelle, UMR 6543, Bât. de Biochimie,
Université de Nice, Parc Valrose, 06108 Nice Cedex 2, France
tél : 04 92 07 69 47
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