[BioC] Problem of read Illumina bead array data in R 2.12.0

[Mark Dunning]

Hi,

Yes, unfortunately this is a bug introduced in the new version of
beadarray. The error is triggered when no qcFile is specified in
readBeadSummaryData. If you have a qcFile then the code should run Ok.

The bug is easy to fix and I will commit the fix in the latest version
within the next day or so.

Best wishes,

Mark

On Wed, Oct 20, 2010 at 7:59 AM,  <jrwang at itri.org.tw> wrote:
> I have a R program reading  data file of Illmina Human Whole Genome Bead Array.
>
> BSData = readBeadSummaryData(dataFile = dataFile, ProbeID="PROBE_ID", skip=0)
>
> This line works fine in R 2.11.1, but not in R 2.12.0.  It gives me something like
>
> Error in readBeadSummaryData(dataFile = dataFile, ProbeID = "PROBE_ID",  :
>  object 'QC' not found
> A bug in new beadarray package maybe? Any Comment?
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i386-pc-mingw32/i386 (32-bit)
> locale:
> [1] LC_COLLATE=Chinese_Taiwan.950  LC_CTYPE=Chinese_Taiwan.950    LC_MONETARY=Chinese_Taiwan.950
> [4] LC_NUMERIC=C                   LC_TIME=Chinese_Taiwan.950
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] beadarray_2.0.0 Biobase_2.10.0
> loaded via a namespace (and not attached):
> [1] limma_3.6.0
> Weihsin Wang, Ph.D.
> Bioinformatics Core Lab.,
> Biomedical Engineering Research Lab.,
> Industrial Technology Research Institute
> TEL:886-3-5913689
> FAX: 886-3-5820445
>
>
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