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. -- Nicolas Servant Equipe Bioinformatique Institut Curie 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE Email: Nicolas.Servant at curie.fr Tel: 01 53 10 70 55 http://bioinfo.curie.fr/

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. >