Entry: HumRef8
Aliases: HumRef8
Keywords: datasets
Description: A mapping file of Illumina Probe IDs to control type
URL: ../../../library/BeadExplorer/html/HumRef8v1.html

Entry: HumWG6
Aliases: HumWG6
Keywords: datasets
Description: A mapping file of Illumina Probe IDs to control type
URL: ../../../library/BeadExplorer/html/HumWG6v1.html

Entry: addManifest
Aliases: addManifest
Keywords: methods
Description: Add annotation data
URL: ../../../library/BeadExplorer/html/addManifest.html

Entry: batchAnalysis
Aliases: batchAnalysis
Keywords: methods
Description: Batch Analysis
URL: ../../../library/BeadExplorer/html/batchAnalysis.html

Entry: beadAnalysis
Aliases: beadAnalysis
Keywords: methods
Description: Automated Bead Analysis
URL: ../../../library/BeadExplorer/html/beadAnalysis.html

Entry: Accessors
Aliases: detExprs fileOrigin nGenes normMethod nSamples param sampleQC signalMeans
Keywords: misc
Description: Accessor Methods for beadData class
URL: ../../../library/BeadExplorer/html/beadData-accessor.html

Entry: beadData-class
Aliases: beadData-class [,beadData-method boxplot,beadData-method detectionCalls,beadData-method detExprs,beadData-method fileOrigin,beadData-method nGenes,beadData-method normMethod,beadData-method nSamples,beadData-method pairs,beadData-method param,beadData-method plot,beadData,missing-method signalMeans,beadData-method summary,beadData-method
Keywords: classes
Description: Class "beadData"
URL: ../../../library/BeadExplorer/html/beadData-class.html

Entry: beadQC-class
Aliases: beadQC-class [,beadQC-method annotation,beadQC-method annotation<-,beadQC-method annotation<-,beadQC,ANY-method fileOrigin,beadQC-method sampleQC,beadQC-method
Keywords: classes
Description: Class "beadQC"
URL: ../../../library/BeadExplorer/html/beadQC-class.html

Entry: boxplotArrays
Aliases: boxplotArrays
Keywords: hplot
Description: Plot a series of QC boxplots
URL: ../../../library/BeadExplorer/html/boxplotArrays.html

Entry: boxplotQC
Aliases: boxplotQC
Keywords: hplot
Description: Plot a subset of QC boxplots
URL: ../../../library/BeadExplorer/html/boxplotQC.html

Entry: clusterplot
Aliases: clusterplot
Keywords: hplot
Description: Plots a hierarchical cluster plot
URL: ../../../library/BeadExplorer/html/clusterplot.html

Entry: cutoff
Aliases: cutoff
Keywords: methods
Description: Determine the number of transcripts that pass a fold change cut-off criteria
URL: ../../../library/BeadExplorer/html/cutoff.html

Entry: detectionCalls
Aliases: detectionCalls
Keywords: methods
Description: Get percentage of genes called present
URL: ../../../library/BeadExplorer/html/detectionCalls.html

Entry: dotplotArrays
Aliases: dotplotArrays
Keywords: hplot
Description: Plots a series of dotplots for BeadChip QC data
URL: ../../../library/BeadExplorer/html/dotplotArrays.html

Entry: dotplotQC
Aliases: dotplotQC
Keywords: hplot
Description: Plot a subset of QC dotplots
URL: ../../../library/BeadExplorer/html/dotplotQC.html

Entry: examplebeadData
Aliases: examplebeadData
Keywords: datasets
Description: An example of a beadData object
URL: ../../../library/BeadExplorer/html/examplebeadData.html

Entry: examplebeadQC
Aliases: examplebeadQC
Keywords: datasets
Description: An example of a beadQC object
URL: ../../../library/BeadExplorer/html/examplebeadQC.html

Entry: extract
Aliases: extract
Keywords: methods
Description: Extract columns from a BeadStudio file
URL: ../../../library/BeadExplorer/html/extract.html

Entry: filterData
Aliases: filterData
Keywords: methods
Description: Filter data based on detection score
URL: ../../../library/BeadExplorer/html/filterData.html

Entry: getAnnot
Aliases: getAnnot
Keywords: methods
Description: Get annotation information
URL: ../../../library/BeadExplorer/html/getAnnot.html

Entry: getArrayStats
Aliases: getArrayStats
Keywords: methods
Description: Get QC values for a BeadChip
URL: ../../../library/BeadExplorer/html/getArrayStats.html

Entry: getDet
Aliases: getDet
Keywords: methods
Description: Get detection scores for a given gene(s)
URL: ../../../library/BeadExplorer/html/getDet.html

Entry: getExprs
Aliases: getExprs
Keywords: methods
Description: Get expression intensities for a given gene(s)
URL: ../../../library/BeadExplorer/html/getExprs.html

Entry: getID
Aliases: getID
Keywords: methods
Description: Get expression data for a given gene ID
URL: ../../../library/BeadExplorer/html/getID.html

Entry: getQC
Aliases: getQC
Keywords: methods
Description: Generate QC data
URL: ../../../library/BeadExplorer/html/getQC.html

Entry: getQC2
Aliases: getQC2
Keywords: methods
Description: Generate QC data
URL: ../../../library/BeadExplorer/html/getQC2.html

Entry: htmloutput
Aliases: htmloutput
Keywords: methods
Description: Produce an html summary report
URL: ../../../library/BeadExplorer/html/htmloutput.html

Entry: multiDensity
Aliases: multiDensity
Keywords: hplot
Description: Plot multiple density functions
URL: ../../../library/BeadExplorer/html/multiDensity.html

Entry: multiecdf
Aliases: multiecdf
Keywords: hplot
Description: Plot multiple estimated cumulative density function graphs
URL: ../../../library/BeadExplorer/html/multiecdf.html

Entry: normalise
Aliases: normalise
Keywords: methods
Description: Normalise a beadData object
URL: ../../../library/BeadExplorer/html/normalise.html

Entry: pc
Aliases: pc
Keywords: hplot
Description: Principal component plot
URL: ../../../library/BeadExplorer/html/pc.html

Entry: plotSamples
Aliases: plotSamples
Keywords: hplot
Description: QC sample plots
URL: ../../../library/BeadExplorer/html/plotSamples.html

Entry: readBead
Aliases: readBead
Keywords: methods
Description: Read BeadStudio expression data file
URL: ../../../library/BeadExplorer/html/readBead.html

Entry: readManifest
Aliases: readManifest
Keywords: methods
Description: Read annotation data
URL: ../../../library/BeadExplorer/html/readManifest.html

Entry: readQC
Aliases: readQC
Keywords: methods
Description: Reads log file data
URL: ../../../library/BeadExplorer/html/readQC.html

Entry: scatterPlot
Aliases: scatterPlot
Keywords: hplot
Description: Pairwise scattergraph of data
URL: ../../../library/BeadExplorer/html/scatterPlot.html

Entry: write.beadData
Aliases: write.beadData
Keywords: methods
Description: Write beadData to a file
URL: ../../../library/BeadExplorer/html/write.beadData.html

Entry: writeQC
Aliases: writeQC
Keywords: methods
Description: Writes QC data to a log file
URL: ../../../library/BeadExplorer/html/writeQC.html
