Is there an annotation package available that uses the ProbeID as the identifier rather than the TargetID as in illuminaRatv1? Thanks -----Original Message----- From: Matt Ritchie [mailto:Matt.Ritchie@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, 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=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 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 > > P Think before you print > This e-mail transmission and any attachments that accompany it may > contain information that is privileged, confidential or otherwise > exempt from disclosure under applicable law and is intended solely for > the use of the > individual(s) to whom it was intended to be addressed. > If you have received this e-mail by mistake, or you are not the > intended recipient, any disclosure, dissemination, distribution, > copying or other use or retention of this communication or its > substance is prohibited. If you have received this communication in > error, please immediately reply to the author via e-mail that you > received this message by mistake and also permanently delete the > original and all copies of this e-mail and any attachments from your computer. Thank you. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor