{
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  "Package": "beadarray",
  "Title": "Quality assessment and low-level analysis for Illumina BeadArray\ndata",
  "Version": "2.63.0",
  "Date": "2026-03-18",
  "Author": "Mark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt\nRitchie",
  "Maintainer": "Mark Dunning <m.dunning@imperial.ac.uk>",
  "Description": "The package is able to read bead-level data (raw TIFFs and\ntext files) output by BeadScan as well as bead-summary data\nfrom BeadStudio. Methods for quality assessment and low-level\nanalysis are provided.",
  "License": "MIT + file LICENSE",
  "biocViews": "Microarray, OneChannel, QualityControl, Preprocessing",
  "LazyData": "yes",
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  "Repository": "https://grimbough.r-universe.dev",
  "Date/Publication": "2026-04-28 12:31:35 UTC",
  "RemoteUrl": "https://git.bioconductor.org/packages/beadarray",
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  "RemoteSha": "b07d5670abeefe7b8bbca8d31d55476927a10fc7",
  "NeedsCompilation": "yes",
  "Packaged": {
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    "User": "root"
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  "MD5sum": "39f893535c42372fe24ea93d1388cbfa",
  "_user": "grimbough",
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  "_created": "2026-06-04T11:17:32.000Z",
  "_published": "2026-06-04T11:47:37.909Z",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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    "login": "markdunning",
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    "description": "https://profiles.imperial.ac.uk/m.dunning",
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    "onechannel",
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    "type": "user",
    "name": "Mike Smith",
    "description": "Data Engineer at Boehringer-Ingelheim"
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  "_exports": [
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    "annotation",
    "annotation<-",
    "ArrayWeights",
    "ArrayWeights<-",
    "backgroundCorrectSingleSection",
    "BASH",
    "BASHCompact",
    "BASHDiffuse",
    "BASHExtended",
    "beadarrayUsersGuide",
    "beadStatusVector",
    "boxplot",
    "calculateDetection",
    "calculateOutlierStats",
    "checkPlatform",
    "checkRegistration",
    "combine",
    "combinedControlPlot",
    "ContrastMatrix",
    "ContrastMatrix<-",
    "controlProbeDetection",
    "convertBeadLevelList",
    "createGEOMatrix",
    "createGEOMeta",
    "createTargetsFile",
    "DesignMatrix",
    "DesignMatrix<-",
    "Detection",
    "Detection<-",
    "expressionQCPipeline",
    "exprs",
    "exprs<-",
    "generateNeighbours",
    "genericBeadIntensityPlot",
    "getAnnotation",
    "getBeadData",
    "greenChannel",
    "greenChannelTransform",
    "HULK",
    "identifyControlBeads",
    "illuminaBackground",
    "illuminaForeground",
    "illuminaOutlierMethod",
    "illuminaSharpen",
    "imageplot",
    "insertBeadData",
    "insertSectionData",
    "limmaDE",
    "LogFC",
    "LogFC<-",
    "logGreenChannelTransform",
    "LogOdds",
    "LogOdds<-",
    "logRatioTransform",
    "logRedChannelTransform",
    "makeControlProfile",
    "makeGEOSubmissionFiles",
    "makeQCTable",
    "medianBackground",
    "medianNormalise",
    "metrics",
    "nObservations",
    "nObservations<-",
    "noOutlierMethod",
    "normaliseIllumina",
    "numBeads",
    "outlierplot",
    "p95",
    "plotBeadIntensities",
    "plotBeadLocations",
    "plotChipLayout",
    "plotMAXY",
    "plotTIFF",
    "poscontPlot",
    "processSwathData",
    "PValue",
    "PValue<-",
    "qcData",
    "quickSummary",
    "readBeadSummaryData",
    "readIdatFiles",
    "readIllumina",
    "readLocsFile",
    "readSampleSheet",
    "readTIFF",
    "redChannelTransform",
    "removeBeadData",
    "se.exprs",
    "se.exprs<-",
    "sectionNames",
    "setAnnotation",
    "setWeights",
    "show",
    "showArrayMask",
    "snr",
    "squeezedVarOutlierMethod",
    "suggestAnnotation",
    "summarize",
    "weightsOutlierMethod"
  ],
  "_datasets": [
    {
      "name": "metaTemplate",
      "title": "GEO required fields",
      "object": "metaTemplate",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "platformSigs",
      "title": "Annotation definitions",
      "object": "platformSigs",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "beadarray-package",
      "title": "The beadarray package: a tool for low-level analysis of Illumina BeadArrays",
      "topics": [
        "beadarray-package"
      ]
    },
    {
      "page": "addFeatureData",
      "title": "Add probe data",
      "topics": [
        "addFeatureData"
      ]
    },
    {
      "page": "annotationInterface",
      "title": "Storage of annotation information",
      "topics": [
        "annotation",
        "annotation,beadLevelData-method",
        "annotation,ExpressionSetIllumina-method",
        "annotation<-,beadLevelData,character-method",
        "annotation<-,ExpressionSetIllumina,character-method",
        "getControlProfile",
        "suggestAnnotation"
      ]
    },
    {
      "page": "backgroundCorrectSingleSection",
      "title": "Background correct an array-section",
      "topics": [
        "backgroundCorrectSingleSection"
      ]
    },
    {
      "page": "BASH",
      "title": "BASH - BeadArray Subversion of Harshlight",
      "topics": [
        "BASH"
      ]
    },
    {
      "page": "BASHCompact",
      "title": "BASH - Compact Defect Analysis",
      "topics": [
        "BASHCompact"
      ]
    },
    {
      "page": "BASHDiffuse",
      "title": "BASH - Diffuse Defect Analysis",
      "topics": [
        "BASHDiffuse"
      ]
    },
    {
      "page": "BASHExtended",
      "title": "BASH - Extended Defect Analysis",
      "topics": [
        "BASHExtended"
      ]
    },
    {
      "page": "beadarrayUsersGuide",
      "title": "View beadarray User's Guide",
      "topics": [
        "beadarrayUsersGuide"
      ]
    },
    {
      "page": "plotBeadIntensities",
      "title": "Plotting the intensities of selected beads on a section",
      "topics": [
        "genericBeadIntensityPlot",
        "plotBeadIntensities"
      ]
    },
    {
      "page": "class-beadLevelData",
      "title": "Class \"beadLevelData\"",
      "topics": [
        "beadLevelData-class",
        "boxplot,beadLevelData-method",
        "numBeads,beadLevelData-method",
        "sectionNames,beadLevelData-method",
        "[[,beadLevelData,ANY,missing-method"
      ]
    },
    {
      "page": "class-BeadLevelList",
      "title": "Class \"BeadLevelList\"",
      "topics": [
        "arrayNames,BeadLevelList-method",
        "BeadLevelList-class",
        "getArrayData,BeadLevelList-method"
      ]
    },
    {
      "page": "class-beadRegistrationData",
      "title": "Class \"beadRegistrationData\"",
      "topics": [
        "beadRegistrationData-class",
        "boxplot,beadRegistrationData-method"
      ]
    },
    {
      "page": "boxplot",
      "title": "Boxplots from summary data",
      "topics": [
        "boxplot,ExpressionSetIllumina-method"
      ]
    },
    {
      "page": "calculateDetection",
      "title": "Calculate detection scores",
      "topics": [
        "calculateDetection"
      ]
    },
    {
      "page": "calculateOutlierStats",
      "title": "Outlier distribution stats",
      "topics": [
        "calculateOutlierStats"
      ]
    },
    {
      "page": "checkRegistration",
      "title": "Perform check for misregistered array segments.",
      "topics": [
        "checkRegistration"
      ]
    },
    {
      "page": "combine",
      "title": "Combine two objects.",
      "topics": [
        "combine,beadLevelData,beadLevelData-method",
        "combine,ExpressionSetIllumina,ExpressionSetIllumina-method"
      ]
    },
    {
      "page": "controlProbeDetection",
      "title": "Percentage of beads detected",
      "topics": [
        "controlProbeDetection"
      ]
    },
    {
      "page": "convertBeadLevelList",
      "title": "Convert a BeadLevelList object into a beadLevelData object",
      "topics": [
        "convertBeadLevelList"
      ]
    },
    {
      "page": "createTargetsFile",
      "title": "A function to generate a targets file given a directory of Illumina bead-level files",
      "topics": [
        "createTargetsFile"
      ]
    },
    {
      "page": "deprecatedFunctions",
      "title": "Deprecated Functions",
      "topics": [
        "arrayNames",
        "checkPlatform",
        "createBeadSummaryData",
        "getAnnotation",
        "getArrayData",
        "setAnnotation"
      ]
    },
    {
      "page": "dim",
      "title": "Retrieve the dimensions of an object",
      "topics": [
        "dim,beadLevelData-method",
        "dim,ExpressionSetIllumina-method"
      ]
    },
    {
      "page": "expressionQCPipeline",
      "title": "Flexible bead-level QC pipeline",
      "topics": [
        "combinedControlPlot",
        "expressionQCPipeline"
      ]
    },
    {
      "page": "class-ExpressionSetIllumina",
      "title": "Class \"ExpressionSetIllumina\"",
      "topics": [
        "Detection",
        "Detection,ExpressionSetIllumina-method",
        "Detection<-",
        "Detection<-,ExpressionSetIllumina,matrix-method",
        "ExpressionSetIllumina-class",
        "exprs,ExpressionSetIllumina-method",
        "exprs<-,ExpressionSetIllumina,matrix-method",
        "nObservations",
        "nObservations,ExpressionSetIllumina-method",
        "nObservations<-",
        "nObservations<-,ExpressionSetIllumina,matrix-method",
        "qcData",
        "qcData,ExpressionSetIllumina-method",
        "se.exprs,ExpressionSetIllumina-method",
        "se.exprs<-,ExpressionSetIllumina,matrix-method",
        "[,ExpressionSetIllumina,ANY-method",
        "[,ExpressionSetIllumina-method"
      ]
    },
    {
      "page": "generateNeighbours",
      "title": "Generate matrix of neighbouring beads",
      "topics": [
        "generateNeighbours"
      ]
    },
    {
      "page": "getBeadData",
      "title": "Get raw data from a beadLevelData object",
      "topics": [
        "getBeadData"
      ]
    },
    {
      "page": "HULK",
      "title": "HULK - Bead Array Normalization by NEighbourhood Residuals",
      "topics": [
        "HULK"
      ]
    },
    {
      "page": "identifyControlBeads",
      "title": "Classify each bead according to its control status",
      "topics": [
        "beadStatusVector",
        "identifyControlBeads"
      ]
    },
    {
      "page": "class-illuminaChannel",
      "title": "Class \"illuminaChannel\"",
      "topics": [
        "greenChannel",
        "illuminaChannel-class"
      ]
    },
    {
      "page": "illuminaOutlierMethod",
      "title": "Identifier outliers on an array section",
      "topics": [
        "illuminaOutlierMethod"
      ]
    },
    {
      "page": "imageplot",
      "title": "imageplot for beadLevelData object",
      "topics": [
        "imageplot"
      ]
    },
    {
      "page": "imageProcessing",
      "title": "Image processing functions",
      "topics": [
        "illuminaBackground",
        "illuminaForeground",
        "illuminaSharpen",
        "medianBackground"
      ]
    },
    {
      "page": "insertBeadData",
      "title": "Add, modify or remove data in a beadLevelData object",
      "topics": [
        "insertBeadData",
        "removeBeadData"
      ]
    },
    {
      "page": "insertSectionData",
      "title": "Modify the sectionData slot",
      "topics": [
        "insertSectionData"
      ]
    },
    {
      "page": "limmaDE",
      "title": "Differential expression using limma",
      "topics": [
        "limmaDE"
      ]
    },
    {
      "page": "class-limmaResults",
      "title": "Class \"limmaResults\"",
      "topics": [
        "ArrayWeights",
        "ArrayWeights,limmaResults-method",
        "ArrayWeights<-",
        "ArrayWeights<-,limmaResults,numeric-method",
        "ContrastMatrix",
        "ContrastMatrix,limmaResults-method",
        "ContrastMatrix<-",
        "ContrastMatrix<-,limmaResults,matrix-method",
        "DesignMatrix",
        "DesignMatrix,limmaResults-method",
        "DesignMatrix<-",
        "DesignMatrix<-,limmaResults,matrix-method",
        "dim,limmaResults-method",
        "limmaResults-class",
        "LogFC",
        "LogFC,limmaResults-method",
        "LogFC<-",
        "LogFC<-,limmaResults,matrix-method",
        "LogOdds",
        "LogOdds,limmaResults-method",
        "LogOdds<-",
        "LogOdds<-,limmaResults,matrix-method",
        "plot,limmaResults-method",
        "PValue",
        "PValue,limmaResults-method",
        "PValue<-",
        "PValue<-,limmaResults,matrix-method",
        "[,limmaResults-method"
      ]
    },
    {
      "page": "GEO",
      "title": "Create files for a Gene Expression Omnibus submission",
      "topics": [
        "createGEOMatrix",
        "createGEOMeta",
        "makeGEOSubmissionFiles"
      ]
    },
    {
      "page": "makeControlProfile",
      "title": "Retrieve control beads",
      "topics": [
        "makeControlProfile"
      ]
    },
    {
      "page": "makeQCTable",
      "title": "Tabulate QC scores",
      "topics": [
        "makeQCTable"
      ]
    },
    {
      "page": "medianNormalise",
      "title": "Median normalise data in a matrix",
      "topics": [
        "medianNormalise"
      ]
    },
    {
      "page": "GEOtemplate",
      "title": "GEO required fields",
      "topics": [
        "metaTemplate"
      ]
    },
    {
      "page": "metrics",
      "title": "Accessing metrics information in bead-level objects",
      "topics": [
        "metrics",
        "metrics,beadLevelData-method",
        "p95",
        "p95,beadLevelData,character-method",
        "snr",
        "snr,beadLevelData,character-method"
      ]
    },
    {
      "page": "noOutlierMethod",
      "title": "returns no outliers on an array section",
      "topics": [
        "noOutlierMethod"
      ]
    },
    {
      "page": "normaliseIllumina",
      "title": "Normalise Illumina expression data",
      "topics": [
        "normaliseIllumina"
      ]
    },
    {
      "page": "numBeads",
      "title": "Gets the number of beads from a beadLevelData object",
      "topics": [
        "numBeads"
      ]
    },
    {
      "page": "outlierplot",
      "title": "Plot outlier locations",
      "topics": [
        "outlierplot"
      ]
    },
    {
      "page": "platformSigs",
      "title": "Annotation definitions",
      "topics": [
        "platformSigs"
      ]
    },
    {
      "page": "plotBeadLocations",
      "title": "Plot bead locations",
      "topics": [
        "plotBeadLocations"
      ]
    },
    {
      "page": "plotChipLayout",
      "title": "Function to Plot the Layout of an Illumina BeadChip",
      "topics": [
        "plotChipLayout"
      ]
    },
    {
      "page": "maplots",
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