[BioC] Empty featureData slot in beadsummary IlluminaExpressionSet object

Johnstone, Alice Alice.Johnstone at esr.cri.nz
Tue Jan 15 21:52:41 CET 2008

Is there an annotation package available that uses the ProbeID as the
identifier rather than the TargetID as in illuminaRatv1? 

-----Original Message-----
From: Matt Ritchie [mailto:Matt.Ritchie at cancer.org.uk] 
Sent: Tuesday, 15 January 2008 3:34 p.m.
To: Johnstone, Alice; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Empty featureData slot in beadsummary
IlluminaExpressionSet object

Hi Alice,

I believe the solution is to set ProbeID="ProbeID" rather than
"TargetID" in readBeadSummaryData().  The row names of the exprs slot in
the ExpressionSetIllumina object are taken from the column specified by
the 'ProbeID' argument and need to be unique for each row.  If they
aren't, the row names are set to row numbers. TargetIDs are not
necessarily unique (occurs when two different probes map to the same
transcript), whereas the ProbeIDs should be (it is a good idea to export
this column from BeadStudio).

I don't think we use the featureData slot for anything at the moment, so
it should be empty. 

I hope this helps.  Best wishes,


> Hello,
> The IlluminaExpressionSet object that I have created from beadsummary 
> data does not have the ProbeIDs attached as the rownames.
> The featureData slot is empty, and hence I just have a sequential 
> rownumber as the identifier instead.
> I tried an upgrade to the dev version but the probeIDs were also not 
> attached.
> How can I fix this?
> Command and session info below,
> Thanks
> Alice
> BSData<-readBeadSummaryData(dataFile,qcFile=qcFile,sampleSheet=sampleS
> he
> et,
> +
> header=TRUE,skip=7,ProbeID="TargetID",columns=list(exprs="AVG_Signal",
> se .exprs="BEAD_STDEV",NoBeads="Avg_NBEADS"
> +
> ,Detection="Detection"),qc.columns=list(controlType="TargetID",exprs="
> AV G.Signal",Detection="Detection"),qc.sep="\t",sep="\t",qc.skip=0,
> + annoPkg="illuminaRatv1")
>> BSData
> ExpressionSetIllumina (storageMode: list)
> assayData: 22517 features, 15 samples
>   element names: exprs, se.exprs, NoBeads, Detection, Narrays, 
> arrayStDev, DiffScore phenoData
>   rowNames: 1, 2, ..., 15  (15 total)
>   varLabels and varMetadata description:
>     Array: Array
>     X: X
>     X.1: X.1
>     Rat: Rat
> featureData
>   featureNames: 
>   fvarLabels and fvarMetadata description: none
> experimentData: use 'experimentData(object)'
> Annotation: illuminaRatv1
> QC Information
>  Available Slots:  exprs se.exprs Detection NoBeads controlType
>   featureNames: 1, 2, ..., 6, 7
>   sampleNames: X1814671016_A.AVG_Signal, X1814671016_B.AVG_Signal, 
> ..., X1814671034_D.AVG_Signal, X1814671034_E.AVG_Signal
>> sessionInfo()
> R version 2.6.1 (2007-11-26)
> 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] tools     stats     graphics  grDevices utils     datasets
> base     
> other attached packages:
>  [1] illuminaRatv1_1.4.0  beadarray_1.6.0      affy_1.16.0
> preprocessCore_1.0.0 affyio_1.6.1
>  [6] geneplotter_1.16.0   lattice_0.17-2       annotate_1.16.1
> xtable_1.5-2         AnnotationDbi_1.0.6
> [11] RSQLite_0.6-4        DBI_0.2-4            Biobase_1.16.2
> limma_2.12.0     
> loaded via a namespace (and not attached):
> [1] grid_2.6.1         KernSmooth_2.22-21 RColorBrewer_1.0-2
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