[BioC] Normalisation GCRMA Error

[Ben Bolstad]

I notice that you are using the previous software release. If this is a
bug we would of course like to get it fixed promptly. If possible could
you try repeating this on the current release (BioC 1.9 on R 2.4.0) and
calling the  read.probematrix() function directly

library(affy)
x <- read.probematrix(filenames=list.celfiles())

Best,

Ben


On Fri, 2006-10-13 at 18:29 +0200, Nicolas Servant wrote:
> Hi all,
> 
> I used GCRMA to normalize 200 arrays HG-U133A with succes. In order to 
> avoid the potential memory problemes, i use a R64 bits version (2.31) 
> with GCRMA 2.4.1
> But when I try to normalize 300 HG-U133-plus2 arrays, I have a 
> segmentation fault :
> 
> Loading required package: affy
> Loading required package: Biobase
> Loading required package: tools
> 
> Welcome to Bioconductor
> 
>     Vignettes contain introductory material. To view, type
>     'openVignette()' or start with 'help(Biobase)'. For details
>     on reading vignettes, see the openVignette help page.
> 
> Loading required package: affyio
> Loading required package: gcrma
> Loading required package: matchprobes
> 
> Computing affinities.Done. *** caught segfault ***
> address 0, cause 'memory not mapped'
> 
> Traceback:
>  1: .Call("read_probeintensities", filenames, rm.mask, rm.outliers,     rm.extra, ref.cdfName, dim.intensity, verbose, cdfInfo, which,     PACKAGE = "affyio")
>  2: read.probematrix(filenames = filenames, which = "pm", cdfname = cdfname)
>  3: fast.bkg(filenames = filenames, pm.affinities = pm.affinities,     mm.affinities = mm.affinities, index.affinities = index.affinities,     type = type, minimum = minimum, optical.correct = optical.correct,     verbose = verbose, k = k, rho = rho, correction = correction,     stretch = stretch, fast = fast, cdfname = cdfname)
>  4: just.gcrma(filenames = l$filenames, phenoData = l$phenoData,     description = l$description, notes = notes, compress = compress,     verbose = verbose, normalize = normalize, bgversion = bgversion,     affinity.info = affinity.info, type = type, k = k, stretch = stretch,     correction = correction, rho = rho, optical.correct = optical.correct,     fast = fast, minimum = minimum, optimize.by = optimize.by,     cdfname = cdfname)
>  5: justGCRMA(filenames = filenames, celfile.path = celfile.path,     type = "affinities")
>  6: normAffy(files$filenames, celfile.path = dataPath, NormMethod)
> aborting ...
> 
> The "read_probeintensities" C function seems to have some problemes ...
> Does anybody know if the number of arrays is limited in GCRMA ? or why i 
> have a segmentation fault !
> Thanks,
> 
> Best,
> Nicolas S.
>