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Hello;
I am using the readBeadSummary function to load in my data using two files: data and control probe files (as shown in the vignette example). While I can run it with no errors when I view the ExpressionSet object there appears to be no QC data loaded under 'QC Information' (see below). Where is the data stored?
Thanks, Meeta
datafile <- file.path(metaDir, "sample_probe_profile.csv") qcfile <- file.path(metaDir, "control_probes.csv") beadData <- readBeadSummaryData(dataFile = datafile, qcFile = qcfile, sep=",", ProbeID = "PROBE_ID", skip = 0, columns = list(exprs ="AVG_Signal", Detection = "Detection_Pval", se.exprs = "BEAD_STDERR", nObservations = "Avg_NBEADS"), qc.skip = 0, qc.sep =",", controlID = "ProbeID", qc.columns = list(exprs = "AVG_Signal", Detection ="Detection_Pval"), annoCols=c("PROBE_ID", "SYMBOL","ENTREZ_GENE_ID","CHROMOSOME"))
> beadData ExpressionSetIllumina (storageMode: list) assayData: 26526 features, 24 samples element names: exprs, se.exprs, nObservations, Detection protocolData: none phenoData rowNames: 9974433081_A 9974433081_B ... 9982502025_H (24 total) varLabels: sampleID varMetadata: labelDescription featureData featureNames: ILMN_2896528 ILMN_2721178 ... 7650601 (26526 total) fvarLabels: ProbeID PROBE_ID ... Status (6 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: QC Information Available Slots: QC Items: sampleNames: