ControlID Qcinfo slot in Illumina beadarray summary data?
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@johnstone-alice-2290
Last seen 7.7 years ago
Hi Stuck at the beginning(!) reading in my Illumina summary data using: > dataFile="ROD-AJ-BeadStudioV2_Sample_Probe_Profile.csv" > qcFile="ControlGeneProfile.txt" > sampleSheet="sampleSheet.txt" > BSData<-readBeadSummaryData(dataFile,qcFile=qcFile,sampleSheet=sampleS he et, + header=TRUE,ProbeID="TargetID",skip=7,columns=list(exprs="AVG_Signal", Be adStDev="BEAD_STDEV", + NoBeads="Avg_NBEADS"),qc.columns=list(ControlID="TargetID",exprs="AVG. Si gnal",Detection="Detection"), + qc.sep=",",sep=",") Did not find a slot called : ControlID In the help for readBeadSummaryData it has a ControlID slot for the qcFile listed, am I missing something? > sessionInfo() R version 2.5.1 (2007-06-27) 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] "grid" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: beadarray beadarraySNP quantsmooth lodplot quantreg SparseM "1.4.0" "1.2.0" "1.2.0" "1.1" "4.08" "0.73" affy affyio geneplotter lattice annotate Biobase "1.14.2" "1.4.1" "1.14.0" "0.15-11" "1.14.1" "1.14.1" limma "2.10.5" Thanks Alice Johnstone PhD Candidate Institute of Environmental Science and Research Ltd Kenepuru Science Centre 34 Kenepuru Drive PO Box 50-348 Porirua New Zealand Tel: + 64 4 914-0717 Fax: + 64 4 914-0770
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio • 847 views
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Mark Dunning ▴ 320
@mark-dunning-1634
Last seen 7.7 years ago
Hi, Unfortunately, this is a bug with version 1.4.0 of beadarray. It will try and read the TargetID column from the quality control file, but there is no slot in the BSData object to put this information in. And this is the message that beadarray gives. Anyways, the BSData object should still be valid and you will be able to do analysis on it. You will be just missing information about which type of control (eg biotin control, negative control....) each of the rows in the qcFile represent, but this can be easily imported separately if you need it. Hope this helps and thanks for bringing the bug to my attention. Regards, Mark On 8 Aug 2007, at 02:13, Johnstone, Alice wrote: > Hi > Stuck at the beginning(!) reading in my Illumina summary data using: > >> dataFile="ROD-AJ-BeadStudioV2_Sample_Probe_Profile.csv" >> qcFile="ControlGeneProfile.txt" >> sampleSheet="sampleSheet.txt" >> > BSData<-readBeadSummaryData > (dataFile,qcFile=qcFile,sampleSheet=sampleShe > et, > + > header=TRUE,ProbeID="TargetID",skip=7,columns=list > (exprs="AVG_Signal",Be > adStDev="BEAD_STDEV", > + > NoBeads="Avg_NBEADS"),qc.columns=list > (ControlID="TargetID",exprs="AVG.Si > gnal",Detection="Detection"), > + qc.sep=",",sep=",") > Did not find a slot called : ControlID > > In the help for readBeadSummaryData it has a ControlID slot for the > qcFile listed, am I missing something? > >> sessionInfo() > R version 2.5.1 (2007-06-27) > 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] "grid" "tools" "stats" "graphics" "grDevices" > "utils" > > [7] "datasets" "methods" "base" > > other attached packages: > beadarray beadarraySNP quantsmooth lodplot quantreg > SparseM > "1.4.0" "1.2.0" "1.2.0" "1.1" "4.08" > "0.73" > affy affyio geneplotter lattice annotate > Biobase > "1.14.2" "1.4.1" "1.14.0" "0.15-11" "1.14.1" > "1.14.1" > limma > "2.10.5" > > > > > Thanks > > Alice Johnstone > PhD Candidate > Institute of Environmental Science and Research Ltd > Kenepuru Science Centre > 34 Kenepuru Drive > PO Box 50-348 > Porirua > New Zealand > Tel: + 64 4 914-0717 > Fax: + 64 4 914-0770 > > _______________________________________________ > 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
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