[BioC] subscript out of bounds error when following new beadarray tutorial

[Mark Dunning]

Hi Moritz,

Thanks for your report. The problem was caused by readBeadSummary data
not correctly setting the channelData slot of the
ExpressionSetIllumina class, so the dimensions of the object could not
be displayed properly. The bug should be fixed now and will appear in
an updated version of the package in the next day or so.

In fact. the only consequence of the bug is the way that the object is
displayed. The rest of the vignette should work fine.

Regards,

Mark

On Thu, Nov 4, 2010 at 10:17 AM, Moritz Kebschull <endothel at gmail.com> wrote:
> Dear list,
>
> I am trying to follow the new bead-summary tutorial
>
> http://www.bioconductor.org/packages/release/bioc/vignettes/beadarray/inst/doc/beadsummary.pdf
>
> However, I end up with a ‘subscript out of bounds’ error. Does anyone happen
> to know what´s wrong?
>
>> library(beadarray)
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Welcome to beadarray version 2.0.1
> There have been major changes to beadarray since Bioconductor 2.6 (April
> 2010). Please see package vignette for details
>> dataFile = "AsuragenMAQC-probe-raw.txt"
>> qcFile = "AsuragenMAQC-controls.txt"
>> BSData = readBeadSummaryData(dataFile = dataFile, qcFile = qcFile,
> controlID = "ProbeID", skip = 0, qc.skip = 0, qc.columns = list(exprs =
> "AVG_Signal",Detection = "Detection Pval"))
> Warning message:
> In readQC(file = qcFile, sep = qc.sep, skip = qc.skip, columns = qc.columns,
>  :
>  controlIDs non-unique: 6 repeated entries have been removed.
>
>> BSData
> ExpressionSetIllumina (storageMode: list)
> Error in object at channelData[[1]] : subscript out of bounds
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] beadarray_2.0.1 Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] limma_3.6.6
>>
>
> Many thanks,
>
> cheers, Moritz
>
>
> Moritz Kebschull
> Fellow
> Clinical Research Unit 208
> University of Bonn, Germany
>
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