[BioC] Empty featureData slot in beadsummary IlluminaExpressionSet object

Johnstone, Alice Alice.Johnstone at esr.cri.nz
Tue Jan 15 02:33:23 CET 2008

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
How can I fix this?
Command and session info below,

+ annoPkg="illuminaRatv1")
> BSData
ExpressionSetIllumina (storageMode: list)
assayData: 22517 features, 15 samples 
  element names: exprs, se.exprs, NoBeads, Detection, Narrays,
arrayStDev, DiffScore 
  rowNames: 1, 2, ..., 15  (15 total)
  varLabels and varMetadata description:
    Array: Array
    X: X
    X.1: X.1
    Rat: Rat
  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) 

LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New
Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252

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

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

loaded via a namespace (and not attached):
[1] grid_2.6.1         KernSmooth_2.22-21 RColorBrewer_1.0-2

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