[BioC] crlmm problem

[Matt Ritchie]

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 at 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 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
>
>
>
>

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