[BioC] crlmm problem

[Aaerp]

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 écrit :
> 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
>
>
>
>