[BioC] Empty featureData slot in beadsummary IlluminaExpressionSet object

[Matt Ritchie]

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,

Matt

> 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=sampleShe
> 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  methods
> 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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