[BioC] crlmm and Affymetrix SNP5 array [genotyping issues]
beniltoncarvalho at gmail.com
Mon Mar 26 18:09:04 CEST 2012
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.
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!!
>> cdfName <- "genomewidesnp5"
>> celPath <- "input"
>> outDir <- "output"
>> Listfiles <- list.celfiles()
>> batch <- as.factor(rep("A",length(Listfiles)))
>> 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
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>  LC_CTYPE=en_US.utf8 LC_NUMERIC=C
>  LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
>  LC_MONETARY=C LC_MESSAGES=en_US.utf8
>  LC_PAPER=en_US.utf8 LC_NAME=C
>  LC_ADDRESS=C LC_TELEPHONE=C
>  LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
> attached base packages:
>  tools stats graphics grDevices utils datasets methods
>  base
> other attached packages:
>  genomewidesnp5Crlmm_1.0.4 ff_2.2-2
>  bit_1.1-7 crlmm_1.10.0
>  oligoClasses_1.14.0 Biobase_2.12.2
> loaded via a namespace (and not attached):
>  affyio_1.20.0 annotate_1.30.0 AnnotationDbi_1.14.1
>  Biostrings_2.20.1 DBI_0.2-5 ellipse_0.3-5
>  genefilter_1.34.0 IRanges_1.10.4 mvtnorm_0.9-9991
>  preprocessCore_1.14.0 RSQLite_0.9-4 splines_2.13.0
>  survival_2.36-9 xtable_1.5-6
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