[BioC] beadarray example data problem

[Keith Satterley]

Hi Mark or anyone else who can help with the beadarray package,

I'm having trouble getting the beadarray example data to work as described:
 > sessionInfo()
R version 2.4.0 (2006-10-03)
i386-pc-mingw32

locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils" 
"datasets"  "base"

other attached packages:
beadarray      affy    affyio   Biobase     limma
   "1.2.1"  "1.12.0"   "1.2.0"  "1.12.0"   "2.9.1"


When I load the BSData item and look at BSData, I have the following:
=====================
 > data(BSData)
 > BSData
ExpressionSetIllumina (storageMode: list)
assayData: 47293 features, 18 samples
   element names: exprs, BeadStDev, NoBeads, Detection
phenoData
   rowNames: I.1, IC.1, ..., P42.2 (18 total)
   varLabels and varMetadata:
     Sample_Name: Sample_Name
     Sample_Well: Sample_Well
     ...: ...
     Sentrix_Position: Sentrix_Position
     (7 total)
featureData
   featureNames: GI_10047089-S, GI_10047091-S, ..., trpF (47293 total)
   varLabels and varMetadata: none
experimentData: use 'experimentData(object)'
Annotation [1] "Illumina"
QC Information
  Available Slots:  Signal StDev Detection
   featureNames: 1475542110_F, 1475542113_E, 1475542114_A, ..., 1475542113_D, 
1475542113_F
   sampleNames: Biotin, cy3_high, cy3_low, ..., pm, negative
=====================
When I extract the data files from Rdata.zip in the package's data directory and 
run the following commands from the Example.R file, I have the following:
=====================
 > targets = readBeadSummaryTargets("targets.txt")
 > targets
       DataFile               SampleSheet              QCInfo
1 raw_data.csv raw_data_sample_sheet.csv raw_data_qcinfo.csv
 > BSData <- readBeadSummaryData(targets)
Reading file  raw_data.csv
Reading file  raw_data.csv
 > BSData
ExpressionSetIllumina (storageMode: list)
assayData: 47293 features, 18 samples
   element names: exprs, BeadStDev, NoBeads, Detection
phenoData
   rowNames: IH.1, IC.1, ..., P42.2 (18 total)
   varLabels and varMetadata:
     Sample_Name: Sample_Name
     Sample_Well: Sample_Well
     ...: ...
     Sentrix_Position: Sentrix_Position
     (7 total)
featureData
   featureNames: 1, 2, ..., 47293 (47293 total)
   varLabels and varMetadata: none
experimentData: use 'experimentData(object)'
Annotation character(0)
QC Information
  Available Slots:
   featureNames: 1475542110_F, 1475542113_E, 1475542114_A, ..., 1475542113_D, 
1475542113_F
   sampleNames: Biotin, cy3_high, cy3_low, ..., pm, negative
=====================

My problem is that I don't have the Target ID's in this second approach. In 
particular note that featureNames in the second approach are not set to the 
TargetIDs as they are in the BSData item.

Can you help me solve this problem,

cheers,

Keith

========================
Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia