crlmm problem
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Aaerp ▴ 40
@aaerp-6373
Last seen 4.1 years ago
France
Hi all, I am trying to analyze some Illumina beadarray SNP data (humanomniexpress12v1b) using crlmm. Do you have any thoughts on what might be happening here? Kind regards, Agusti library(crlmm) library(ff) ocProbesets(150e3) datadir <- "/Volumes/My Passport/SNP_LGG/6182351100" samplesheet = read.csv(file.path(datadir, "SampleSheet_PJ1111109_11S46v2.csv"), header=TRUE, as.is=TRUE,sep="\t") arrayNames <- file.path(datadir, unique(samplesheet[, "SentrixPosition_A"])) all(file.exists(paste(arrayNames, "_Grn.idat", sep=""))) #[1] TRUE all(file.exists(paste(arrayNames, "_Red.idat", sep=""))) #[1] TRUE cdfName <- "humanomniexpress12v1b" batch <- rep("1", nrow(samplesheet)) arrayInfo <- list(barcode=NULL, position="SentrixPosition_A") cnSet <- genotype.Illumina(sampleSheet=samplesheet, arrayNames=arrayNames, arrayInfoColNames=arrayInfo, cdfName="humanomniexpress12v1b", batch=batch) Instantiate CNSet container. path arg not set. Assuming files are in local directory, or that complete path is provided Initializing container for genotyping and copy number estimation Loading required package: humanomniexpress12v1bCrlmm Welcome to humanomniexpress12v1bCrlmm version 1.0.1 reading /Volumes/My Passport/SNP_LGG/6182351100/R01C01_Grn.idat Erreur dans G$RunInfo[1, 1] : indice hors limites sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8 attached base packages: [1] tools parallel stats graphics grDevices utils datasets methods base other attached packages: [1] ff_2.2-12 bit_1.1-10 humanomniexpress12v1bCrlmm_1.0.1 [4] crlmm_1.20.1 preprocessCore_1.22.0 oligoClasses_1.22.0 [7] BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affyio_1.28.0 Biobase_2.20.1 BiocInstaller_1.10.4 Biostrings_2.28.0 codetools_0.2-8 [6] ellipse_0.3-8 foreach_1.4.1 GenomicRanges_1.12.5 grid_3.0.2 illuminaio_0.2.0 [11] IRanges_1.18.4 iterators_1.0.6 lattice_0.20-23 Matrix_1.1-1.1 matrixStats_0.8.12 [16] mvtnorm_0.9-9996 R.methodsS3_1.5.2 RcppEigen_0.3.2.0 stats4_3.0.2 VGAM_0.9-3 [21] zlibbioc_1.6.0
SNP beadarray crlmm SNP beadarray crlmm • 905 views
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Aaerp ▴ 40
@aaerp-6373
Last seen 4.1 years ago
France
In English will be better... Best regards, Agusti Instantiate CNSet container. path arg not set. Assuming files are in local directory, or that complete path is provided Initializing container for genotyping and copy number estimation reading /Volumes/My Passport/SNP_LGG/6182351100/R01C01_Grn.idat Error in G$RunInfo[1, 1] : subscript out of bounds Le 01/02/2014 11:27, Aaerp a ?crit : > Hi all, > > I am trying to analyze some Illumina beadarray SNP data > (humanomniexpress12v1b) using crlmm. Do you have any thoughts on what > might be happening here? > > Kind regards, > Agusti > > library(crlmm) > library(ff) > > ocProbesets(150e3) > > datadir <- "/Volumes/My Passport/SNP_LGG/6182351100" > samplesheet = read.csv(file.path(datadir, > "SampleSheet_PJ1111109_11S46v2.csv"), header=TRUE, as.is=TRUE,sep="\t") > > arrayNames <- file.path(datadir, unique(samplesheet[, > "SentrixPosition_A"])) > > all(file.exists(paste(arrayNames, "_Grn.idat", sep=""))) > #[1] TRUE > all(file.exists(paste(arrayNames, "_Red.idat", sep=""))) > #[1] TRUE > cdfName <- "humanomniexpress12v1b" > batch <- rep("1", nrow(samplesheet)) > arrayInfo <- list(barcode=NULL, position="SentrixPosition_A") > > cnSet <- genotype.Illumina(sampleSheet=samplesheet, > arrayNames=arrayNames, > arrayInfoColNames=arrayInfo, > cdfName="humanomniexpress12v1b", > batch=batch) > > Instantiate CNSet container. > path arg not set. Assuming files are in local directory, or that > complete path is provided > Initializing container for genotyping and copy number estimation > Loading required package: humanomniexpress12v1bCrlmm > Welcome to humanomniexpress12v1bCrlmm version 1.0.1 > reading /Volumes/My Passport/SNP_LGG/6182351100/R01C01_Grn.idat > Erreur dans G$RunInfo[1, 1] : indice hors limites > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8 > > attached base packages: > [1] tools parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] ff_2.2-12 bit_1.1-10 humanomniexpress12v1bCrlmm_1.0.1 > [4] crlmm_1.20.1 preprocessCore_1.22.0 oligoClasses_1.22.0 > [7] BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.28.0 Biobase_2.20.1 BiocInstaller_1.10.4 > Biostrings_2.28.0 codetools_0.2-8 > [6] ellipse_0.3-8 foreach_1.4.1 GenomicRanges_1.12.5 > grid_3.0.2 illuminaio_0.2.0 > [11] IRanges_1.18.4 iterators_1.0.6 lattice_0.20-23 > Matrix_1.1-1.1 matrixStats_0.8.12 > [16] mvtnorm_0.9-9996 R.methodsS3_1.5.2 RcppEigen_0.3.2.0 > stats4_3.0.2 VGAM_0.9-3 > [21] zlibbioc_1.6.0 > > > >
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Dear Agusti, This sounds like a problem with importing the idats. If you can send through (offline) some Red and Green idat files for a few samples I can take a closer look. Best wishes, Matt ----- Original Message ----- From: "Aaerp" <al3n70rn@gmail.com> To: "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> Cc: bioconductor at r-project.org Sent: Saturday, 1 February, 2014 9:39:20 PM Subject: Re: [BioC] crlmm problem In English will be better... Best regards, Agusti Instantiate CNSet container. path arg not set. Assuming files are in local directory, or that complete path is provided Initializing container for genotyping and copy number estimation reading /Volumes/My Passport/SNP_LGG/6182351100/R01C01_Grn.idat Error in G$RunInfo[1, 1] : subscript out of bounds Le 01/02/2014 11:27, Aaerp a ?crit : > Hi all, > > I am trying to analyze some Illumina beadarray SNP data > (humanomniexpress12v1b) using crlmm. Do you have any thoughts on what > might be happening here? > > Kind regards, > Agusti > > library(crlmm) > library(ff) > > ocProbesets(150e3) > > datadir <- "/Volumes/My Passport/SNP_LGG/6182351100" > samplesheet = read.csv(file.path(datadir, > "SampleSheet_PJ1111109_11S46v2.csv"), header=TRUE, as.is=TRUE,sep="\t") > > arrayNames <- file.path(datadir, unique(samplesheet[, > "SentrixPosition_A"])) > > all(file.exists(paste(arrayNames, "_Grn.idat", sep=""))) > #[1] TRUE > all(file.exists(paste(arrayNames, "_Red.idat", sep=""))) > #[1] TRUE > cdfName <- "humanomniexpress12v1b" > batch <- rep("1", nrow(samplesheet)) > arrayInfo <- list(barcode=NULL, position="SentrixPosition_A") > > cnSet <- genotype.Illumina(sampleSheet=samplesheet, > arrayNames=arrayNames, > arrayInfoColNames=arrayInfo, > cdfName="humanomniexpress12v1b", > batch=batch) > > Instantiate CNSet container. > path arg not set. Assuming files are in local directory, or that > complete path is provided > Initializing container for genotyping and copy number estimation > Loading required package: humanomniexpress12v1bCrlmm > Welcome to humanomniexpress12v1bCrlmm version 1.0.1 > reading /Volumes/My Passport/SNP_LGG/6182351100/R01C01_Grn.idat > Erreur dans G$RunInfo[1, 1] : indice hors limites > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8 > > attached base packages: > [1] tools parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] ff_2.2-12 bit_1.1-10 humanomniexpress12v1bCrlmm_1.0.1 > [4] crlmm_1.20.1 preprocessCore_1.22.0 oligoClasses_1.22.0 > [7] BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.28.0 Biobase_2.20.1 BiocInstaller_1.10.4 > Biostrings_2.28.0 codetools_0.2-8 > [6] ellipse_0.3-8 foreach_1.4.1 GenomicRanges_1.12.5 > grid_3.0.2 illuminaio_0.2.0 > [11] IRanges_1.18.4 iterators_1.0.6 lattice_0.20-23 > Matrix_1.1-1.1 matrixStats_0.8.12 > [16] mvtnorm_0.9-9996 R.methodsS3_1.5.2 RcppEigen_0.3.2.0 > stats4_3.0.2 VGAM_0.9-3 > [21] zlibbioc_1.6.0 > > > > _______________________________________________ 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}
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