[BioC] beadarray: Error when reading control probe profile with readBeadSummaryData

[Mark Dunning]

Hi Moritz,

Looking at the code, it seems that beadarray is expecting a column
called TargetID in the QC file. I think this indicates what type of
control (e.g. negative, housekeeping each line represents). Do you
have such a column in your file? I'm afraid the code in beadarray
isn't robust to the situation where this column doesn't exist.

Regards,

Mark

On Thu, Jan 13, 2011 at 4:10 PM, Moritz Kebschull <endothel at gmail.com> wrote:
> Dear list,
>
> when I try to read the Illumina beadarray control probe profile using
> readBeadSummaryData
>
> library(beadarray)
> dataFile = "Spag4_data.txt"
> qcFile = "Spag4_con.txt"
> BSData = readBeadSummaryData(dataFile = dataFile, dec=",", qcFile = qcFile,
> skip = 0, qc.skip = 0)
>
> I get
>
> Error in if (!is.na(typeCol)) { : argument is of length zero
>
> Does anyone know what this could mean?
> The error must be related to the qcFile, when I skip reading it everything
> works as expected...
>
> Many thanks,
>
> Moritz (Fellow, University of Bonn, Germany)
>
>
> My sessionInfo()
>
> R version 2.12.0 (2010-10-15)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
> [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
> [5] LC_TIME=German_Germany.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] beadarray_2.0.2 Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] limma_3.6.9  tools_2.12.0
>
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