[BioC] ControlID Qcinfo slot in Illumina beadarray summary data?

[Mark Dunning]

Hi,

Unfortunately, this is a bug with version 1.4.0 of beadarray. It will  
try and read the TargetID column from the quality control file, but  
there is no slot in the BSData object to put this information in. And  
this is the message that beadarray gives.

Anyways, the BSData object should still be valid and you will be able  
to do analysis on it. You will be just missing information about  
which type of control (eg biotin control, negative control....) each  
of the rows in the qcFile represent, but this can be easily imported  
separately if you need it.

Hope this helps and thanks for bringing the bug to my attention.

Regards,

Mark

On 8 Aug 2007, at 02:13, Johnstone, Alice wrote:

> Hi
> Stuck at the beginning(!) reading in my Illumina summary data using:
>
>> dataFile="ROD-AJ-BeadStudioV2_Sample_Probe_Profile.csv"
>> qcFile="ControlGeneProfile.txt"
>> sampleSheet="sampleSheet.txt"
>>
> BSData<-readBeadSummaryData 
> (dataFile,qcFile=qcFile,sampleSheet=sampleShe
> et,
> +
> header=TRUE,ProbeID="TargetID",skip=7,columns=list 
> (exprs="AVG_Signal",Be
> adStDev="BEAD_STDEV",
> +
> NoBeads="Avg_NBEADS"),qc.columns=list 
> (ControlID="TargetID",exprs="AVG.Si
> gnal",Detection="Detection"),
> + qc.sep=",",sep=",")
> Did not find a slot called : ControlID
>
> In the help for readBeadSummaryData it has a ControlID slot for the
> qcFile listed, am I missing something?
>
>> sessionInfo()
> R version 2.5.1 (2007-06-27)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New
> Zealand.1252;LC_MONETARY=English_New
> Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252
>
> attached base packages:
> [1] "grid"      "tools"     "stats"     "graphics"  "grDevices"  
> "utils"
>
> [7] "datasets"  "methods"   "base"
>
> other attached packages:
>    beadarray beadarraySNP  quantsmooth      lodplot     quantreg
> SparseM
>      "1.4.0"      "1.2.0"      "1.2.0"        "1.1"       "4.08"
> "0.73"
>         affy       affyio  geneplotter      lattice     annotate
> Biobase
>     "1.14.2"      "1.4.1"     "1.14.0"    "0.15-11"     "1.14.1"
> "1.14.1"
>        limma
>     "2.10.5"
>
>
>
>
>  Thanks
>
> Alice Johnstone
> PhD Candidate
> Institute of Environmental Science and Research Ltd
> Kenepuru Science Centre
> 34 Kenepuru Drive
> PO Box 50-348
> Porirua
> New Zealand
> Tel:  + 64 4 914-0717
> Fax: + 64 4 914-0770
>
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