{
  "_id": "6a1af9011d7bb097a09fb3ef",
  "Package": "lumi",
  "Type": "Package",
  "Title": "BeadArray Specific Methods for Illumina Methylation and\nExpression Microarrays",
  "Version": "2.65.0",
  "Date": "2020-10-02",
  "Author": "Pan Du, Richard Bourgon, Gang Feng, Simon Lin",
  "Maintainer": "Lei Huang <lhuang1998@gmail.com>",
  "Description": "The lumi package provides an integrated solution for the\nIllumina microarray data analysis. It includes functions of\nIllumina BeadStudio (GenomeStudio) data input, quality control,\nBeadArray-specific variance stabilization, normalization and\ngene annotation at the probe level. It also includes the\nfunctions of processing Illumina methylation microarrays,\nespecially Illumina Infinium methylation microarrays.",
  "License": "LGPL (>= 2)",
  "LazyLoad": "yes",
  "biocViews": "Microarray, OneChannel, Preprocessing, DNAMethylation,\nQualityControl, TwoChannel",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:47:48 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:32:06 UTC",
  "RemoteUrl": "https://github.com/bioc/lumi",
  "RemoteRef": "HEAD",
  "RemoteSha": "13fc7d349d5059424e05594b5c99594a0d3e78aa",
  "MD5sum": "34b55d28767824afb53a1c4d5a52d4ee",
  "_user": "bioc",
  "_type": "src",
  "_file": "lumi_2.65.0.tar.gz",
  "_fileid": "939e4bb9df8d7c2fb4243213e25b23c188e336972980c3d4d5d90778246bdda2",
  "_filesize": 8767838,
  "_sha256": "939e4bb9df8d7c2fb4243213e25b23c188e336972980c3d4d5d90778246bdda2",
  "_created": "2026-05-30T09:47:48.000Z",
  "_published": "2026-05-30T14:49:37.600Z",
  "_jobs": [
    {
      "job": 78640690410,
      "time": 356,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7307523636"
    },
    {
      "job": 78640690407,
      "time": 572,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307543264"
    },
    {
      "job": 78640690408,
      "time": 651,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307550846"
    },
    {
      "job": 78640690414,
      "time": 344,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7308999921"
    },
    {
      "job": 78640690412,
      "time": 357,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7309002373"
    },
    {
      "job": 78639869282,
      "time": 430,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307298862"
    },
    {
      "job": 78640690409,
      "time": 335,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307521974"
    },
    {
      "job": 78640690424,
      "time": 689,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307552601"
    },
    {
      "job": 78640690430,
      "time": 849,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7307568867"
    },
    {
      "job": 78640690417,
      "time": 527,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307537151"
    }
  ],
  "_bioccheck": {
    "error": 3,
    "warning": 5,
    "note": 17
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676653717",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/lumi",
  "_commit": {
    "id": "13fc7d349d5059424e05594b5c99594a0d3e78aa",
    "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",
    "time": 1777379526
  },
  "_maintainer": {
    "name": "Lei Huang",
    "email": "lhuang1998@gmail.com",
    "login": "lxhuang7",
    "description": "",
    "uuid": 13385652
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "version": ">= 2.5.5",
      "role": "Depends"
    },
    {
      "package": "affy",
      "version": ">= 1.23.4",
      "role": "Imports"
    },
    {
      "package": "methylumi",
      "version": ">= 2.3.2",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "annotate",
      "role": "Imports"
    },
    {
      "package": "lattice",
      "role": "Imports"
    },
    {
      "package": "mgcv",
      "version": ">= 1.4-0",
      "role": "Imports"
    },
    {
      "package": "nleqslv",
      "role": "Imports"
    },
    {
      "package": "KernSmooth",
      "role": "Imports"
    },
    {
      "package": "preprocessCore",
      "role": "Imports"
    },
    {
      "package": "RSQLite",
      "role": "Imports"
    },
    {
      "package": "DBI",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "stats4",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "beadarray",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "vsn",
      "role": "Suggests"
    },
    {
      "package": "lumiBarnes",
      "role": "Suggests"
    },
    {
      "package": "lumiHumanAll.db",
      "role": "Suggests"
    },
    {
      "package": "lumiHumanIDMapping",
      "role": "Suggests"
    },
    {
      "package": "genefilter",
      "role": "Suggests"
    },
    {
      "package": "RColorBrewer",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 10,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.65.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.64.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "microarray",
    "onechannel",
    "preprocessing",
    "dnamethylation",
    "qualitycontrol",
    "twochannel"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 2054,
    "source": "https://www.bioconductor.org/packages/stats/bioc/lumi"
  },
  "_mentions": 238,
  "_searchresults": 350,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/lumi.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addAnnotationInfo",
    "addControlData2lumi",
    "addControlData2methyLumiM",
    "addNuId2lumi",
    "addNuID2lumi",
    "adjColorBias.quantile",
    "adjColorBias.ssn",
    "asBigMatrix",
    "beadNum",
    "beadNum<-",
    "beta2m",
    "bgAdjust",
    "bgAdjustMethylation",
    "boxplot",
    "boxplotColorBias",
    "coerce",
    "colorBiasSummary",
    "combine",
    "controlData",
    "controlData<-",
    "density",
    "detection",
    "detection<-",
    "detectionCall",
    "detectOutlier",
    "estimateBeta",
    "estimateIntensity",
    "estimateLumiCV",
    "estimateM",
    "estimateMethylationBG",
    "exprs",
    "exprs<-",
    "gammaFitEM",
    "getChipInfo",
    "getChrInfo",
    "getControlData",
    "getControlProbe",
    "getControlType",
    "getHistory",
    "getNuIDMappingInfo",
    "hist",
    "id2seq",
    "IlluminaID2nuID",
    "importMethyIDAT",
    "inverseVST",
    "is.nuID",
    "lumiB",
    "lumiExpresso",
    "lumiMethyB",
    "lumiMethyC",
    "lumiMethyN",
    "lumiMethyR",
    "lumiMethyStatus",
    "lumiN",
    "lumiQ",
    "lumiR",
    "lumiR.batch",
    "lumiT",
    "m2beta",
    "MAplot",
    "methylationCall",
    "normalizeMethylation.quantile",
    "normalizeMethylation.ssn",
    "nuID2EntrezID",
    "nuID2IlluminaID",
    "nuID2probeID",
    "nuID2RefSeqID",
    "nuID2targetID",
    "pairs",
    "plot",
    "plotCDF",
    "plotColorBias1D",
    "plotColorBias2D",
    "plotControlData",
    "plotDensity",
    "plotGammaFit",
    "plotHousekeepingGene",
    "plotSampleRelation",
    "plotStringencyGene",
    "plotVST",
    "probeID2nuID",
    "produceGEOPlatformFile",
    "produceGEOSampleInfoTemplate",
    "produceGEOSubmissionFile",
    "produceMethylationGEOSubmissionFile",
    "rankinvariant",
    "rsn",
    "sampleNames<-",
    "se.exprs",
    "se.exprs<-",
    "seq2id",
    "show",
    "smoothQuantileNormalization",
    "ssn",
    "summary",
    "targetID2nuID",
    "vst"
  ],
  "_datasets": [
    {
      "name": "example.lumi",
      "title": "Example Illumina Expression data in LumiBatch class",
      "object": "example.lumi",
      "file": "example.lumi.rda",
      "class": [
        "LumiBatch"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "example.lumiMethy",
      "title": "Example Illumina Infinium Methylation data in MethyLumiM class",
      "object": "example.lumiMethy",
      "file": "example.lumiMethy.rda",
      "class": [
        "MethyLumiM"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "example.methyTitration",
      "title": "Example Illumina Infinium Methylation titration data in MethyLumiM class",
      "object": "example.methyTitration",
      "file": "example.methyTitration.rda",
      "class": [
        "MethyLumiM"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "lumi.package",
      "title": "A package for preprocessing Illumina microarray data",
      "topics": [
        "lumi-package",
        "lumi"
      ]
    },
    {
      "page": "addAnnotationInfo",
      "title": "Add probe color channel and basic annotation information based on the annotation library of Illumina methylation microarray",
      "topics": [
        "addAnnotationInfo"
      ]
    },
    {
      "page": "addControlData2lumi",
      "title": "Add the control probe data into the controlData slot of LumiBatch object",
      "topics": [
        "addControlData2lumi"
      ]
    },
    {
      "page": "addControlData2methyLumiM",
      "title": "Add methylation control data to a MethyLumiM object",
      "topics": [
        "addControlData2methyLumiM"
      ]
    },
    {
      "page": "addNuID2lumi",
      "title": "Add the nuID information to the LumiBatch object",
      "topics": [
        "addNuID2lumi",
        "addNuId2lumi"
      ]
    },
    {
      "page": "adjColorBias.quantile",
      "title": "Color bias adjustment of Illumina Infinium methylaton microarrays using smooth quantile normalization",
      "topics": [
        "adjColorBias.quantile"
      ]
    },
    {
      "page": "adjColorBias.ssn",
      "title": "Color bias adjustment of Illumina Infinium methylaton microarrays using simple shift and scaling normalization",
      "topics": [
        "adjColorBias.ssn"
      ]
    },
    {
      "page": "asBigMatrix-methods",
      "title": "convert the data matrix in the assayData of a ExpressionSet as BigMatrix",
      "topics": [
        "asBigMatrix",
        "asBigMatrix,ExpressionSet-method",
        "asBigMatrix-methods"
      ]
    },
    {
      "page": "beta2m",
      "title": "Convert methylation Beta-value to M-value",
      "topics": [
        "beta2m"
      ]
    },
    {
      "page": "bgAdjust",
      "title": "Background adjustment for Illumina data",
      "topics": [
        "bgAdjust"
      ]
    },
    {
      "page": "bgAdjustMethylation",
      "title": "Estimate and adjust the background levels of Illumina Infinium methylaton microarrays",
      "topics": [
        "bgAdjustMethylation"
      ]
    },
    {
      "page": "boxplot-methods",
      "title": "boxplot of a ExpressionSet object",
      "topics": [
        "boxplot,ExpressionSet-method",
        "boxplot-methods",
        "boxplot.ExpressionSet"
      ]
    },
    {
      "page": "boxplot-MethyLumiM-methods",
      "title": "boxplot of a MethyLumiM object",
      "topics": [
        "boxplot,MethyLumiM-method"
      ]
    },
    {
      "page": "boxplotColorBias",
      "title": "Plot the Illumina Infinium methylation color bias in terms of boxplot",
      "topics": [
        "boxplotColorBias"
      ]
    },
    {
      "page": "colorBiasSummary",
      "title": "A summary of colorBias information",
      "topics": [
        "colorBiasSummary"
      ]
    },
    {
      "page": "density-methods",
      "title": "Density plot of a ExpressionSet object",
      "topics": [
        "density,ExpressionSet-method",
        "density-methods",
        "density.ExpressionSet"
      ]
    },
    {
      "page": "detectionCall",
      "title": "Estimate the detectable probe ratio",
      "topics": [
        "detectionCall"
      ]
    },
    {
      "page": "detectOutlier",
      "title": "Detect the outlier sample (or gene)",
      "topics": [
        "detectOutlier"
      ]
    },
    {
      "page": "estimateBeta",
      "title": "Estimate methylation Beta-value matrix",
      "topics": [
        "estimateBeta"
      ]
    },
    {
      "page": "estimateIntensity",
      "title": "Estimate intensity of Illumina methylation data",
      "topics": [
        "estimateIntensity"
      ]
    },
    {
      "page": "estimateLumiCV",
      "title": "Estimate the coefficient of variance matrix of LumiBatch object",
      "topics": [
        "estimateLumiCV"
      ]
    },
    {
      "page": "estimateM",
      "title": "Estimate methylation M-value matrix",
      "topics": [
        "estimateM"
      ]
    },
    {
      "page": "estimateMethylationBG",
      "title": "Estimate the background levels of Illumina Infinium methylaton microarrays",
      "topics": [
        "estimateMethylationBG"
      ]
    },
    {
      "page": "example.lumi",
      "title": "Example Illumina Expression data in LumiBatch class",
      "topics": [
        "example.lumi"
      ]
    },
    {
      "page": "example.lumiMethy",
      "title": "Example Illumina Infinium Methylation data in MethyLumiM class",
      "topics": [
        "example.lumiMethy"
      ]
    },
    {
      "page": "example.methyTitration",
      "title": "Example Illumina Infinium Methylation titration data in MethyLumiM class",
      "topics": [
        "example.methyTitration"
      ]
    },
    {
      "page": "gammaFitEM",
      "title": "Estimate the methylation status by fitting a Gamma mixture model using EM algorithm",
      "topics": [
        "gammaFitEM"
      ]
    },
    {
      "page": "getChipInfo",
      "title": "Get Illumina Chip Information based on probe identifiers",
      "topics": [
        "getChipInfo"
      ]
    },
    {
      "page": "getChrInfo",
      "title": "get the chromosome location information of methylation probes",
      "topics": [
        "getChrInfo"
      ]
    },
    {
      "page": "getControlData",
      "title": "Get control probe information",
      "topics": [
        "getControlData"
      ]
    },
    {
      "page": "getControlProbe",
      "title": "Get the control probe Ids",
      "topics": [
        "getControlProbe"
      ]
    },
    {
      "page": "getControlType",
      "title": "Get the types of the control probes",
      "topics": [
        "getControlType"
      ]
    },
    {
      "page": "getNuIDMappingInfo",
      "title": "get the mapping information from nuID to RefSeq ID",
      "topics": [
        "getNuIDMappingInfo"
      ]
    },
    {
      "page": "hist-methods",
      "title": "Density plot of a ExpressionSet object",
      "topics": [
        "hist,ExpressionSet-method",
        "hist-methods",
        "hist.ExpressionSet"
      ]
    },
    {
      "page": "id2seq",
      "title": "Transfer a nuID as a nucleotide sequence",
      "topics": [
        "id2seq"
      ]
    },
    {
      "page": "IlluminaID2nuID",
      "title": "Matching Illumina IDs to nuID based on Illumina ID mapping library",
      "topics": [
        "IlluminaID2nuID"
      ]
    },
    {
      "page": "importMethyIDAT",
      "title": "Import Illumina methylation .idat files as an MethyLumiM object",
      "topics": [
        "importMethyIDAT"
      ]
    },
    {
      "page": "inverseVST",
      "title": "Inverse VST transform",
      "topics": [
        "inverseVST"
      ]
    },
    {
      "page": "is.nuID",
      "title": "nuID self-identification",
      "topics": [
        "is.nuID"
      ]
    },
    {
      "page": "lumiB",
      "title": "Background correction of Illumina Expression data",
      "topics": [
        "lumiB"
      ]
    },
    {
      "page": "LumiBatch-class",
      "title": "Class LumiBatch: contain and describe Illumina microarray data",
      "topics": [
        "beadNum",
        "beadNum,ExpressionSet-method",
        "beadNum<-",
        "beadNum<-,ExpressionSet,ANY-method",
        "beadNum<-,ExpressionSet-method",
        "class:LumiBatch",
        "combine,ExpressionSet,LumiBatch-method",
        "combine,LumiBatch,ExpressionSet-method",
        "combine,LumiBatch,LumiBatch-method",
        "controlData",
        "controlData,LumiBatch-method",
        "controlData<-",
        "controlData<-,LumiBatch,ANY-method",
        "controlData<-,LumiBatch-method",
        "detection",
        "detection,ExpressionSet-method",
        "detection<-",
        "detection<-,ExpressionSet,ANY-method",
        "detection<-,ExpressionSet-method",
        "getHistory",
        "getHistory,LumiBatch-method",
        "initialize,LumiBatch-method",
        "LumiBatch",
        "LumiBatch-class",
        "sampleNames<-,LumiBatch,ANY-method",
        "se.exprs",
        "se.exprs,ExpressionSet-method",
        "se.exprs<-",
        "se.exprs<-,ExpressionSet,ANY-method",
        "se.exprs<-,ExpressionSet-method",
        "show,LumiBatch-method",
        "summary,LumiBatch-method",
        "[,LumiBatch,ANY,ANY,ANY-method",
        "[,LumiBatch-method"
      ]
    },
    {
      "page": "lumiExpresso",
      "title": "From raw Illumina probe intensities to expression values",
      "topics": [
        "lumiExpresso"
      ]
    },
    {
      "page": "lumiMethyB",
      "title": "Adjust background level of Illumina Infinium methylation data",
      "topics": [
        "lumiMethyB"
      ]
    },
    {
      "page": "lumiMethyC",
      "title": "Color bias adjust of Illumina Infinium methylation data",
      "topics": [
        "lumiMethyC"
      ]
    },
    {
      "page": "lumiMethyN",
      "title": "Normalize the Illumina Infinium methylation data",
      "topics": [
        "lumiMethyN"
      ]
    },
    {
      "page": "lumiMethyR",
      "title": "Reading Illumina methylation microarray data",
      "topics": [
        "lumiMethyR"
      ]
    },
    {
      "page": "lumiMethyStatus",
      "title": "Estimate the methylation status of individual methylation sites",
      "topics": [
        "lumiMethyStatus"
      ]
    },
    {
      "page": "lumiN",
      "title": "Between chip normalization of a LumiBatch object",
      "topics": [
        "lumiN"
      ]
    },
    {
      "page": "lumiQ",
      "title": "Quality control evaluation of the LumiBatch object",
      "topics": [
        "lumiQ"
      ]
    },
    {
      "page": "lumiR",
      "title": "Read in Illumina expression data",
      "topics": [
        "lumiR"
      ]
    },
    {
      "page": "lumiR.batch",
      "title": "Read BeadStudio output files in batch",
      "topics": [
        "lumiR.batch"
      ]
    },
    {
      "page": "lumiT",
      "title": "Transfer the Illumina data to stabilize the variance",
      "topics": [
        "lumiT"
      ]
    },
    {
      "page": "m2beta",
      "title": "Convert methylation M-value to Beta-value",
      "topics": [
        "m2beta"
      ]
    },
    {
      "page": "MAplot-methods",
      "title": "MAplot of a ExpressionSet object",
      "topics": [
        "MAplot",
        "MAplot,ExpressionSet-method",
        "MAplot-methods",
        "MAplot.ExpressionSet"
      ]
    },
    {
      "page": "methylationCall",
      "title": "Estimated methylation call",
      "topics": [
        "methylationCall"
      ]
    },
    {
      "page": "monoSmu",
      "title": "Monotonic smooth method",
      "topics": [
        "monoSmu"
      ]
    },
    {
      "page": "monoSpline",
      "title": "Fitting a curve with monotonic spline",
      "topics": [
        "monoSpline"
      ]
    },
    {
      "page": "normalizeMethylation.quantile",
      "title": "Quantile normalization of Illumina Infinium methylation data at probe level",
      "topics": [
        "normalizeMethylation.quantile"
      ]
    },
    {
      "page": "normalizeMethylation.ssn",
      "title": "Shift and scaling normalization of Illumina Infinium methylation data at probe level",
      "topics": [
        "normalizeMethylation.ssn"
      ]
    },
    {
      "page": "nuID2EntrezID",
      "title": "Map nuID to Entrez ID",
      "topics": [
        "nuID2EntrezID"
      ]
    },
    {
      "page": "nuID2IlluminaID",
      "title": "Matching nuIDs to Illumina IDs based on Illumina ID mapping library",
      "topics": [
        "nuID2IlluminaID"
      ]
    },
    {
      "page": "nuID2probeID",
      "title": "Mapping nuID into Illumina ProbeID",
      "topics": [
        "nuID2probeID"
      ]
    },
    {
      "page": "nuID2RefSeqID",
      "title": "Map nuID to RefSeq ID",
      "topics": [
        "nuID2RefSeqID"
      ]
    },
    {
      "page": "nuID2targetID",
      "title": "Mapping nuID into Illumina TargetID",
      "topics": [
        "nuID2targetID"
      ]
    },
    {
      "page": "pairs-methods",
      "title": "Pair plot of an ExpressionSet object",
      "topics": [
        "pairs,ExpressionSet-method",
        "pairs-methods",
        "pairs.ExpressionSet"
      ]
    },
    {
      "page": "plot-methods",
      "title": "Plot of a ExpressionSet object",
      "topics": [
        "plot,ExpressionSet,missing-method",
        "plot,ExpressionSet-method",
        "plot-methods",
        "plot.ExpressionSet"
      ]
    },
    {
      "page": "plotCDF",
      "title": "plot the cumulative distribution function of a ExpressionSet object",
      "topics": [
        "plotCDF",
        "plotCDF,ExpressionSet-method",
        "plotCDF.ExpressionSet"
      ]
    },
    {
      "page": "plotColorBias1D",
      "title": "Plot the color bias density plot of Illumina Infinium Methylation data",
      "topics": [
        "plotColorBias1D"
      ]
    },
    {
      "page": "plotColorBias2D",
      "title": "Plot the color bias of Illumina Infinium Methylation data in two dimensions",
      "topics": [
        "plotColorBias2D"
      ]
    },
    {
      "page": "plotControlData",
      "title": "Plot the mean expression (with standard deviation bar) of different type of control probes",
      "topics": [
        "plotControlData"
      ]
    },
    {
      "page": "plotDensity",
      "title": "plot the density distribution",
      "topics": [
        "plotDensity",
        "plotDensity.ExpressionSet"
      ]
    },
    {
      "page": "plotGammaFit",
      "title": "plot the fitting results of 'gammaFitEM'",
      "topics": [
        "plotGammaFit"
      ]
    },
    {
      "page": "plotHousekeepingGene",
      "title": "Plot the housekeeping gene expression profile",
      "topics": [
        "plotHousekeepingGene"
      ]
    },
    {
      "page": "plotSampleRelation",
      "title": "visualize the sample relations",
      "topics": [
        "plotSampleRelation"
      ]
    },
    {
      "page": "plotStringencyGene",
      "title": "plot the Stringency related control probe profiles",
      "topics": [
        "plotStringencyGene"
      ]
    },
    {
      "page": "plotVST",
      "title": "plot the VST (Variance Stabilizing Transform) function",
      "topics": [
        "plotVST"
      ]
    },
    {
      "page": "probeID2nuID",
      "title": "Mapping Illumina ProbeID as nuID",
      "topics": [
        "probeID2nuID"
      ]
    },
    {
      "page": "produceGEOPlatformFile",
      "title": "Produce GEO Platform Submission File in SOFT format",
      "topics": [
        "produceGEOPlatformFile"
      ]
    },
    {
      "page": "produceGEOSampleInfoTemplate",
      "title": "Produce the template of GEO sample information",
      "topics": [
        "produceGEOSampleInfoTemplate"
      ]
    },
    {
      "page": "produceGEOSubmissionFile",
      "title": "Produce GEO Sample Submission File in SOFT format",
      "topics": [
        "produceGEOSubmissionFile"
      ]
    },
    {
      "page": "produceMethylationGEOSubmissionFile",
      "title": "Produce GEO Sample Submission File of Illumina methylation microarray data in SOFT format",
      "topics": [
        "produceMethylationGEOSubmissionFile"
      ]
    },
    {
      "page": "rankinvariant",
      "title": "Rank Invariant Normalization",
      "topics": [
        "rankinvariant"
      ]
    },
    {
      "page": "rsn",
      "title": "Robust Spline Normalization between chips",
      "topics": [
        "rsn"
      ]
    },
    {
      "page": "seq2id",
      "title": "Transfer a nucleotide sequence as a nuID",
      "topics": [
        "seq2id"
      ]
    },
    {
      "page": "smoothQuantileNormalization",
      "title": "Smooth quantile normalization",
      "topics": [
        "smoothQuantileNormalization"
      ]
    },
    {
      "page": "ssn",
      "title": "Simple Scaling Normalization",
      "topics": [
        "ssn"
      ]
    },
    {
      "page": "targetID2nuID",
      "title": "Mapping Illumina TargetID (GeneID) into nuID",
      "topics": [
        "targetID2nuID"
      ]
    },
    {
      "page": "vst",
      "title": "Variance Stabilizing Transformation",
      "topics": [
        "vst"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "affy",
    "affyio",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "base64",
    "beanplot",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocManager",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "bumphunter",
    "cachem",
    "cigarillo",
    "cli",
    "clipr",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "DelayedMatrixStats",
    "digest",
    "dir.expiry",
    "doRNG",
    "dplyr",
    "farver",
    "fastmap",
    "FDb.InfiniumMethylation.hg19",
    "filelock",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "genefilter",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "GEOquery",
    "ggplot2",
    "glue",
    "gtable",
    "h5mread",
    "HDF5Array",
    "hms",
    "httr",
    "httr2",
    "illuminaio",
    "IRanges",
    "isoband",
    "iterators",
    "jsonlite",
    "KEGGREST",
    "KernSmooth",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mclust",
    "memoise",
    "methylumi",
    "mgcv",
    "mime",
    "minfi",
    "multtest",
    "nleqslv",
    "nlme",
    "nor1mix",
    "openssl",
    "org.Hs.eg.db",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "preprocessCore",
    "prettyunits",
    "progress",
    "purrr",
    "quadprog",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "readr",
    "rentrez",
    "reshape",
    "reshape2",
    "restfulr",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "Rhtslib",
    "rjson",
    "rlang",
    "rngtools",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "scrime",
    "selectr",
    "Seqinfo",
    "siggenes",
    "snow",
    "SparseArray",
    "sparseMatrixStats",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "TxDb.Hsapiens.UCSC.hg19.knownGene",
    "tzdb",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_score": 6.634819733995179,
  "_indexed": true,
  "_nocasepkg": "lumi",
  "_universes": [
    "bioc",
    "lxhuang7"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.65.0",
      "date": "2026-05-30T10:29:06.000Z",
      "distro": "noble",
      "commit": "13fc7d349d5059424e05594b5c99594a0d3e78aa",
      "fileid": "ebf2a1990dda74fc5600d895f4240e74d5680afef6f96c3143dd04111462e129",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676653717"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.65.0",
      "date": "2026-05-30T10:29:43.000Z",
      "distro": "noble",
      "commit": "13fc7d349d5059424e05594b5c99594a0d3e78aa",
      "fileid": "4c73894a9ae2fb88c3155c30233ca2f38b1c1879eb8d60c259872d1057289cbc",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676653717"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.65.0",
      "date": "2026-05-30T14:45:23.000Z",
      "commit": "13fc7d349d5059424e05594b5c99594a0d3e78aa",
      "fileid": "3060e0e32121c877b4f9cf25b8cf144cbcf1acbca3bbf3c23f0027f7b59a0c8d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676653717"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.65.0",
      "date": "2026-05-30T14:45:50.000Z",
      "commit": "13fc7d349d5059424e05594b5c99594a0d3e78aa",
      "fileid": "97c0bd6f0aa07be4cdfe7272f69b66ddcad0d69d1a85af199e6ae63a09256556",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676653717"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.65.0",
      "date": "2026-05-30T10:29:48.000Z",
      "commit": "13fc7d349d5059424e05594b5c99594a0d3e78aa",
      "fileid": "51089a13c9a9229c7eb389a0fcc66345c373cbe64c6b584080e7ba706dc50e34",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676653717"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.65.0",
      "date": "2026-05-30T10:28:27.000Z",
      "commit": "13fc7d349d5059424e05594b5c99594a0d3e78aa",
      "fileid": "963856d1632628ac0536626a57738b0f94780198c75e18cc7b2cfc5f2089806a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676653717"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.65.0",
      "date": "2026-05-30T10:32:21.000Z",
      "commit": "13fc7d349d5059424e05594b5c99594a0d3e78aa",
      "fileid": "cefb958573499cf1cdf0763f71cd6587064d1b046d223451f5ca6e280caf31fb",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676653717"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.65.0",
      "date": "2026-05-30T10:27:43.000Z",
      "commit": "13fc7d349d5059424e05594b5c99594a0d3e78aa",
      "fileid": "4a5aae519ec4156c4a5bbec8e7c6cf5e5b9a729f6d27e5479ebc75294c14a494",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676653717"
    }
  ]
}