[BioC] crlmm and Affymetrix SNP5 array [genotyping issues]

[Benilton Carvalho]

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.

benilton

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!!
>
>
>> library(crlmm)
>> cdfName <- "genomewidesnp5"
>> celPath <- "input"
>>  outDir <- "output"
>> Listfiles <- list.celfiles()
>> ocProbesets(50e3)
>> batch <- as.factor(rep("A",length(Listfiles)))
>>plate<-substr(basename(Listfiles),1,8)
>> library(ff)
>> 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
>
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>
>  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>  [7] LC_PAPER=en_US.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
>
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] genomewidesnp5Crlmm_1.0.4 ff_2.2-2
>
> [3] bit_1.1-7                 crlmm_1.10.0
> [5] oligoClasses_1.14.0       Biobase_2.12.2
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.20.0         annotate_1.30.0       AnnotationDbi_1.14.1
>
>  [4] Biostrings_2.20.1     DBI_0.2-5             ellipse_0.3-5
>  [7] genefilter_1.34.0     IRanges_1.10.4        mvtnorm_0.9-9991
> [10] preprocessCore_1.14.0 RSQLite_0.9-4         splines_2.13.0
>
> [13] survival_2.36-9       xtable_1.5-6
>
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>
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