[BioC] beadarray without qcFile

Alex Gutteridge alexg at ruggedtextile.com
Thu Nov 11 11:35:15 CET 2010


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,
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:

<     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)

 [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            

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      
 [9] gdata_2.8.0        gtools_2.6.2       beadarray_2.0.0   

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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