
On Nov 16, 2011, at 6:00 AM, bioconductor-request@r-project.org wrote:

> Message: 1
> Date: Tue, 15 Nov 2011 13:20:15 +0100
> From: Francesco Mancuso <francesco.mancuso@crg.eu>
> To: <Bioconductor@r-project.org>
> Subject: [BioC] Possible bug in SNPchip
> Message-ID: <4EC258FF.5020205@crg.eu>
> Content-Type: text/plain
> 
> Hi all!
> I have some problems using SNPchip package.
> 
> When i run the following code
>> oligoSet <- new("oligoSnpSet", copyNumber=as.matrix(CopyNumber),
> call=crlmmCalls, callProbability=crlmmConf, annotation=annotation(crlmmOut))
>> x <- oligoSet[chromosome(oligoSet) %in% as.character(3), c(1,2)]
>> plot(x)
> I obtain the following error:
> 
> Error in plotCytoband(cytoband = cytoband, new = FALSE, cytoband.ycoords = op$cytoband.ycoords,  :
>   subscript out of bounds
> 
> 
> The strange is that if I plot only chromosome 1 (or a set of chromosome
> that start from 1), it works.

Fixed in v 1.18.1 on the release branch, as well as devel (v.19.1).   

Thanks-

Rob

> This is my R session info
> 
> R version 2.14.0 (2011-10-31)
> Platform: i386-pc-mingw32/i386 (32-bit)
> 
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                           LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] grDevices datasets  splines   graphics  stats     tcltk     utils     methods   base
> 
> other attached packages:
>  [1] crlmm_1.12.0             SNPchip_1.18.0           VanillaICE_1.16.1        IRanges_1.12.1           pd.mapping250k.sty_1.4.0 RSQLite_0.10.0           DBI_0.2-5                oligo_1.18.0             oligoClasses_1.16.0
> [10] Biobase_2.14.0           svSocket_0.9-52          TinnR_1.0.3              R2HTML_2.2               Hmisc_3.9-0              survival_2.36-10
> 
> loaded via a namespace (and not attached):
>  [1] affxparser_1.26.1     affyio_1.22.0         annotate_1.32.0       AnnotationDbi_1.16.0  Biostrings_2.22.0     bit_1.1-7           cluster_1.14.1        ellipse_0.3-5         ff_2.2-3              genefilter_1.36.0
> [11] grid_2.14.0           lattice_0.20-1        mvtnorm_0.9-9991      preprocessCore_1.16.0 svMisc_0.9-63         tools_2.14.0   xtable_1.6-0          zlibbioc_1.0.0
> 
> 
> 
> --
> 
> *Francesco Mattia Mancuso*
> Bioinformatician
> 
> - Bioinformatics Core Facility
> - Proteomics Core Facility
> 
> CRG-Centre for Genomic Regulation (Room 439)
> C/ Dr. Aiguader, 88 (Edif. PRBB)
> 08003 Barcelona, Spain


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