Hello everyone, I am doing beadsummary data analysis for illumina's WG-DASL data. I am using beadarray package for analysis. Could anybody tell me why I am not getting "QC Information" for my data as I am also importing qcFile. Here is following script:: ****************************************************** > library(beadarray) > BSData <- readBeadSummaryData(dataFile="SampleProbeProfile.txt",qcFile="ControlP robePr ofile.txt",sep="\t", skip=0, ProbeID="ProbeID", + columns = list(exprs ="AVG_Signal",se.exprs="BEAD_STDERR",nObservations = "Avg_NBEADS", Detection="Detection Pval"), + qc.sep="\t",qc.skip=0, controlID="ProbeID",qc.columns = list(exprs="AVG_Signal", se.exprs="BEAD_STDERR", + nObservations="Avg_NBEADS", Detection="Detection Pval")) Warning message: In readQC(file = qcFile, sep = qc.sep, skip = qc.skip, columns = qc.columns, : controlIDs non-unique: 4 repeated entries have been removed. > BSData ExpressionSetIllumina (storageMode: list) assayData: 29785 features, 12 samples element names: exprs, se.exprs, nObservations, Detection protocolData: none phenoData rowNames: D1R_1 D2NR_1 ... Control_3 (12 total) varLabels: sampleID varMetadata: labelDescription featureData featureNames: 6450255 2570615 ... 7650093 (29785 total) fvarLabels: ProbeID TargetID Status fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: QC Information Available Slots: QC Items: sampleNames: > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] beadarray_2.8.1 ggplot2_0.9.3.1 Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.20.7 BeadDataPackR_1.10.0 colorspace_1.2-1 DBI_0.2-5 dichromat_2.0-0 [6] digest_0.6.3 grid_2.15.2 gtable_0.1.2 IRanges_1.16.6 labeling_0.2 [11] limma_3.14.4 MASS_7.3-22 munsell_0.4 parallel_2.15.2 plyr_1.8 [16] proto_0.3-10 RColorBrewer_1.0-5 reshape2_1.2.2 RSQLite_0.11.2 scales_0.2.3 [21] stats4_2.15.2 stringr_0.6.2 tools_2.15.2 ****************************************************** Thanks, Abdul Rawoof [[alternative HTML version deleted]]