[BioC] Normalisation GCRMA Error
bmb at bmbolstad.com
Sat Oct 14 02:19:16 CEST 2006
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
x <- read.probematrix(filenames=list.celfiles())
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'
> 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 !
> Nicolas S.
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