[BioC] Empty featureData slot in beadsummary IlluminaExpressionSet object
Johnstone, Alice
Alice.Johnstone at esr.cri.nz
Tue Jan 15 02:33:23 CET 2008
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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