Hello mailing list, I'm trying to perform some analysis on SNP5 arrays (Affymetrix) and am running problems for performing genotyping commands. My ultimate aim is to use the genotyping information to perform a subsequent crlmmCopyNumber step in my R code. The analysis progresses smoothly until determining gender estimations and then it shows as error message. Please advise!! > library(crlmm) > cdfName <- "genomewidesnp5" > celPath <- "input" > outDir <- "output" > Listfiles <- list.celfiles() > ocProbesets(50e3) > batch <- as.factor(rep("A",length(Listfiles))) >plate<-substr(basename(Listfiles),1,8) > library(ff) > cnSet <- genotype(filenames = Listfiles, cdfName = "genomewidesnp5", batch = plate) Loading required package:genomewidesnp5Crlmm Welcome to genomewidesnp5Crlmmversion1.0.4 Loading annotations and mixtliure model parameters. Initializing ff objects. Instantiating CNSet container Preprocessing 169 files. Cloning A and B matrices to store genotype calls and confidence scores. Quantile normalizing nonpolymorphicmarkers Processing nonpolymorphic probes for 169 files. Calling 605453 SNPs for recalibration... Loading annotations. Determining gender. Error in nrow(theCenters) : subscript out of bounds > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] genomewidesnp5Crlmm_1.0.4 ff_2.2-2 [3] bit_1.1-7 crlmm_1.10.0 [5] oligoClasses_1.14.0 Biobase_2.12.2 loaded via a namespace (and not attached): [1] affyio_1.20.0 annotate_1.30.0 AnnotationDbi_1.14.1 [4] Biostrings_2.20.1 DBI_0.2-5 ellipse_0.3-5 [7] genefilter_1.34.0 IRanges_1.10.4 mvtnorm_0.9-9991 [10] preprocessCore_1.14.0 RSQLite_0.9-4 splines_2.13.0 [13] survival_2.36-9 xtable_1.5-6 [[alternative HTML version deleted]]

My first recommendation is to upgrade your R installation to the current one (R-2.14.2) and install the latest crlmm package. Then, if the problem is reproducible on the latest version, Rob and I would be in a much better position to dig into the problem. benilton ps: Note that in about 1 week or so, new versions of both R and BioConductor will be released (so, you definitely want this upcoming upgrade as well). On 26 March 2012 05:31, Ali ZAIDI <alizaid12 at="" gmail.com=""> wrote: > Hello mailing list, > > I'm trying to perform some analysis on SNP5 arrays (Affymetrix) and am > running problems for performing genotyping commands. > > My ultimate aim is to use the genotyping information to perform a > subsequent crlmmCopyNumber step in my R code. > > The analysis progresses smoothly until determining gender estimations > and then it shows as error message. > > Please advise!! > > >> library(crlmm) >> cdfName <- "genomewidesnp5" >> celPath <- "input" >> ?outDir <- "output" >> Listfiles <- list.celfiles() >> ocProbesets(50e3) >> batch <- as.factor(rep("A",length(Listfiles))) >>plate<-substr(basename(Listfiles),1,8) >> library(ff) >> cnSet <- genotype(filenames = > Listfiles, cdfName = "genomewidesnp5", batch = plate) > > > Loading required package:genomewidesnp5Crlmm > Welcome to genomewidesnp5Crlmmversion1.0.4 > Loading annotations and mixtliure model parameters. > Initializing ff objects. > Instantiating CNSet container > Preprocessing 169 files. > Cloning A and B matrices to store > genotype calls and confidence scores. > Quantile normalizing nonpolymorphicmarkers > Processing nonpolymorphic probes for 169 files. > Calling 605453 SNPs for recalibration... > Loading annotations. > Determining gender. > Error in nrow(theCenters) : subscript out of bounds > >> sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > ?[1] LC_CTYPE=en_US.utf8 ? ? ? LC_NUMERIC=C > > ?[3] LC_TIME=en_US.utf8 ? ? ? ?LC_COLLATE=en_US.utf8 > ?[5] LC_MONETARY=C ? ? ? ? ? ? LC_MESSAGES=en_US.utf8 > ?[7] LC_PAPER=en_US.utf8 ? ? ? LC_NAME=C > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ?LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] tools ? ? stats ? ? graphics ?grDevices utils ? ? datasets ?methods > [8] base > > other attached packages: > [1] genomewidesnp5Crlmm_1.0.4 ff_2.2-2 > > [3] bit_1.1-7 ? ? ? ? ? ? ? ? crlmm_1.10.0 > [5] oligoClasses_1.14.0 ? ? ? Biobase_2.12.2 > > loaded via a namespace (and not attached): > ?[1] affyio_1.20.0 ? ? ? ? annotate_1.30.0 ? ? ? AnnotationDbi_1.14.1 > > ?[4] Biostrings_2.20.1 ? ? DBI_0.2-5 ? ? ? ? ? ? ellipse_0.3-5 > ?[7] genefilter_1.34.0 ? ? IRanges_1.10.4 ? ? ? ?mvtnorm_0.9-9991 > [10] preprocessCore_1.14.0 RSQLite_0.9-4 ? ? ? ? splines_2.13.0 > > [13] survival_2.36-9 ? ? ? xtable_1.5-6 > > ? ? ? ?[[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