beadarray - QC file loads but doesn't appear in ExpressionSetIllumina object
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meeta.mistry ▴ 20
@meetamistry-7355
Last seen 12 days ago
United States

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: 
beadarray qc • 813 views
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