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
>
>
>
>
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