[BioC] beadarray without qcFile

[Mark Dunning]

Hi Alex,

Thanks for the noticing the bug. It was also noticed just after the
release of beadarray_2.0.0 and subsequently fixed. Trying updating to
the latest version of beadarray.

Regards,

Mark

On Thu, Nov 11, 2010 at 10:35 AM, Alex Gutteridge
<alexg at ruggedtextile.com> wrote:
> Hi,
>
> I'm trying to load some legacy Illumina data where I don't have the
> control/qc file with the new version of beadarray. Whatever I do I seem to
> get an error regarding the QC object:
>
>> BSData2 = readBeadSummaryData(dataFile =
> "../data/MIAMI_MPC_SampleProbeProfile.txt", ProbeID="ProbeID", skip=0,
> qcFile=NULL)
> Error in readBeadSummaryData(dataFile =
> "../data/MIAMI_MPC_SampleProbeProfile.txt",  :
>  object 'QC' not found
>
> >From a quick look at the source it looks like qcFile is checked for null
> in the first instance but then later the QC object itself is checked which
> blows up if the first check failed and so QC was never initialised.
>
> The following simple diff on readBeadSummaryData seems to let it work, but
> perhaps I'm missing some subtle aspect of the original code:
>
> 162c162
> <     if (!is.null(QC) > 0) {
> ---
>>     if (!is.null(qcFile)) {
>
> Session info:
>
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>  [1] pcaMethods_1.32.0  Rcpp_0.8.7         pls_2.1-0          MASS_7.3-8
>
>  [5] RColorBrewer_1.0-2 gplots_2.8.0       caTools_1.10
> bitops_1.0-4.1
>  [9] gdata_2.8.0        gtools_2.6.2       beadarray_2.0.0
> Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] KernSmooth_2.23-4 limma_3.6.0       tools_2.12.0
>
> --
> Alex Gutteridge
>
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