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_M ONETARY=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

Hi Keith, Thanks for letting me know about the problem. I've looked into it and all that was required was to add an "as.character" at the appropriate point when I name the rows in assayData. I made the changes and submitted an updated version to both release and development version of the package. Regards, Mark On 20 Oct 2006, at 03:06, Keith Satterley wrote: > 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 > > _______________________________________________ > 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

To Mark or anyone who can modify the beadarray package, I am having further problems with the example data in the beadarray package. Using R2.4.0 or R2.5.0dev on Windows XP. > sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_M ONETARY=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" "1.12.2" "2.9.1" When I do the following: ================= > library(beadarray) > 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 > QCInfo(BSData) <environment: 0x042ad370=""> ================= When I load the BSData item I get the following: ================= > library(beadarray) > data(BSData) > QCInfo(BSData) $Signal Biotin cy3_high cy3_low cy3_med gene hs house labeling mm pm negative 1475542110_F 7551.0 32436.0 816.6 11178.2 205.8 29498.3 7914.2 92.9 3584.5 21807.1 94.4 ...for 18 lines $StDev Biotin cy3_high cy3_low cy3_med gene hs house labeling mm pm negative 1475542110_F 675.2 9453.7 155.3 3303.9 0.5 5463.8 2405.3 7.6 2978.1 13118.4 11.8 ...for 18 lines $Detection Biotin cy3_high cy3_low cy3_med gene hs house labeling mm pm negative 1475542110_F 1 1 1 1 0.6499011 1 1 0.4153883 1 1 0.7470226 ...for 18 lines ================== So there is something wrong with QCInfo(BSData) in the first approach. I have investigated this problem and found that if I change line 54 in ExpressionSetIlluminaQC.R from: QC = assayDataNew(Signal = signal, StDev=var, Detection=detection, storageMode="list") to QC = as.list(assayDataNew(Signal = signal, StDev=var, Detection=detection, storageMode="list")) the problem is fixed. If Mark or anyone else could check this fix and if they agree, please submit this it to the current release and devel versions of the beadarray package, I'm sure it would help others trying to get the example data to work as descibed, thanks Keith ======================== Keith Satterley Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research Parkville, Melbourne, Victoria, Australia