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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