Dear Bioconductor Hi, I'm Won. I try to do microarray normalization by R. I use justRMA function within affy package, got error about segment fault. I don't know why it happen. I attached error below. Please help me. Thank you. Cheers, Won ======================= OS : Redhat linux Cpu : intel xeon X5570 Memory : 26Gb & OS : Ubuntu Cpu : intel q6600 Memory : 8Gb ======================= Loading required package: Biobase Loading required package: methods Welcome to Bioconductor Vignettes contain introductory material. To view, type 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation("pkgname")'. Loading required package: gcrma Loading required package: preprocessCore Attaching package: 'affyPLM' The following object(s) are masked from 'package:stats': resid, residuals, weights *** caught segfault *** address 0xc609000, cause 'memory not mapped' Traceback: 1: .Call("rma_c_complete", probeintensities$pm, pNList, ngenes, normalize, background, bgversion, verbose, PACKAGE = "affy") 2: just.rma(filenames = l$filenames, phenoData = l$phenoData, description = l$description, notes = notes, compress = compress, rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, verbose = verbose, normalize = normalize, background = background, bgversion = bgversion, destructive = destructive, cdfname = cdfname) 3: justRMA() aborting ... /var/spool/sge/tachyon1145/job_scripts/477103: line 21: 22829 Segmentation fault /home01/e133ywc/R/R-2.13.0/bin/Rscript /scratch/e133ywc/big/198/198.R -- -- Won Cheol Yim, MSc. Doctoral student Plant molecular genetics lab. Dept. of plant biotechnology Graduate School Dongguk University Korea Rep. Contact Cell : +82 10 3853 3926 VoIP : +82 70 8226 3853 Email : ascendo@dongguk.edu Curriculum Vitae : http://ascendo.u.googlepages.com/ Lab page : http://pmgl.dongguk.edu/ fly. [[alternative HTML version deleted]]

>From your error, you've submitted this job to Sun Grid Engine right? Possibly more likely an SGE problem but I'm not sure. Could you try running the script without using SGE? Paul On Tue, Jun 14, 2011 at 2:58 AM, Won Cheol Yim <ascendo at="" dongguk.edu=""> wrote: > Dear Bioconductor > Hi, > > I'm Won. > > I try to do microarray normalization by R. > > I use justRMA function within affy package, got error about segment fault. > > I don't know why it happen. > > I attached error below. > > Please help me. > > Thank you. > > Cheers, > > Won > > ======================= > OS : Redhat linux > Cpu : intel xeon X5570 > Memory : 26Gb > > & > > OS : Ubuntu > Cpu : intel q6600 > Memory : 8Gb > > ======================= > Loading required package: Biobase > Loading required package: methods > > Welcome to Bioconductor > > ?Vignettes contain introductory material. To view, type > ?'browseVignettes()'. To cite Bioconductor, see > ?'citation("Biobase")' and for packages 'citation("pkgname")'. > > Loading required package: gcrma > Loading required package: preprocessCore > > Attaching package: 'affyPLM' > > The following object(s) are masked from 'package:stats': > > ? resid, residuals, weights > > > ?*** caught segfault *** > address 0xc609000, cause 'memory not mapped' > > Traceback: > ?1: .Call("rma_c_complete", probeintensities$pm, pNList, ngenes, > normalize, background, bgversion, verbose, PACKAGE = "affy") > ?2: just.rma(filenames = l$filenames, phenoData = l$phenoData, description = > l$description, ? ? notes = notes, compress = compress, rm.mask = rm.mask, > rm.outliers = rm.outliers, ? ? rm.extra = rm.extra, verbose = verbose, > normalize = normalize, ? ? background = background, bgversion = bgversion, > destructive = destructive, ? ? cdfname = cdfname) > ?3: justRMA() > aborting ... > /var/spool/sge/tachyon1145/job_scripts/477103: line 21: 22829 Segmentation > fault ? ? ?/home01/e133ywc/R/R-2.13.0/bin/Rscript > /scratch/e133ywc/big/198/198.R > > -- > -- > Won Cheol Yim, MSc. > Doctoral student > Plant molecular genetics lab. > Dept. of plant biotechnology > Graduate School > Dongguk University > Korea Rep. > > Contact > Cell : +82 10 3853 3926 > VoIP : +82 70 8226 3853 > Email : ascendo at dongguk.edu > Curriculum Vitae : http://ascendo.u.googlepages.com/ > Lab page : http://pmgl.dongguk.edu/ > ?fly. > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Paul Geeleher (PhD Student) School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com