{
  "_id": "6a13f1feacfb0bcc41d30e42",
  "Package": "affy",
  "Version": "1.91.0",
  "Title": "Methods for Affymetrix Oligonucleotide Arrays",
  "Author": "Rafael A. Irizarry <rafa@ds.dfci.harvard.edu>, Laurent Gautier\n<lgautier@gmail.com>, Benjamin Milo Bolstad\n<bmb@bmbolstad.com>, and Crispin Miller\n<cmiller@picr.man.ac.uk> with contributions from Magnus Astrand\n<Magnus.Astrand@astrazeneca.com>, Leslie M. Cope\n<cope@mts.jhu.edu>, Robert Gentleman, Jeff Gentry, Conrad\nHalling <challing@agilixcorp.com>, Wolfgang Huber, James\nMacDonald <jmacdon@u.washington.edu>, Benjamin I. P.\nRubinstein, Christopher Workman <workman@cbs.dtu.dk>, John\nZhang",
  "Maintainer": "Robert D. Shear <rshear@ds.dfci.harvard.edu>",
  "URL": "https://bioconductor.org/packages/affy",
  "BugReports": "https://github.com/rafalab/affy/issues",
  "Description": "The package contains functions for exploratory\noligonucleotide array analysis. The dependence on tkWidgets\nonly concerns few convenience functions. 'affy' is fully\nfunctional without it.",
  "License": "LGPL (>= 2.0)",
  "Collate": "ProgressBarText.R ppset.ttest.R ppsetApply.R expressoWidget.R\ngetCDFenv.R AffyRNAdeg.R avdiff.R barplot.ProbeSet.R\nbg.Affy.chipwide.R bg.R expresso.R fit.li.wong.R\ngenerateExprVal.method.avgdiff.R\ngenerateExprVal.method.liwong.R generateExprVal.method.mas.R\ngenerateExprVal.method.medianpolish.R\ngenerateExprVal.method.playerout.R hlog.R justrma.R\nloess.normalize.R maffy.R mas5.R merge.AffyBatch.R\nnormalize.constant.R normalize.contrasts.R\nnormalize.invariantset.R normalize.loess.R normalize.qspline.R\nnormalize.quantiles.R pairs.AffyBatch.R plot.density.R\nplotLocation.R plot.ProbeSet.R pmcorrect.mas.R AffyBatch.R\nmva.pairs.R ProbeSet.R read.affybatch.R rma.R summary.R\ntukey.biweight.R whatcdf.R xy2indices.R zzz.R",
  "biocViews": "Microarray, OneChannel, Preprocessing",
  "LazyLoad": "yes",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:30:03 UTC",
  "RemoteUrl": "https://github.com/bioc/affy",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "yes",
  "Packaged": {
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    "User": "root"
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  "_created": "2026-05-25T06:44:06.000Z",
  "_published": "2026-05-25T06:53:50.564Z",
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    "source": "https://www.bioconductor.org/packages/stats/bioc/affy"
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  "_mentions": 989,
  "_devurl": "https://github.com/rafalab/affy",
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  "_assets": [
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    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "extra/NEWS.txt",
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    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/rafalab/affy",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    ".setAffyOptions",
    "$.AffyBatch",
    "affy.scalevalue.exprSet",
    "AffyRNAdeg",
    "AllButCelsForReadAffy",
    "avdiff",
    "barplot",
    "barplot.ProbeSet",
    "bg.adjust",
    "bg.correct",
    "bg.correct.mas",
    "bg.correct.none",
    "bg.correct.rma",
    "bg.parameters",
    "bgcorrect.methods",
    "boxplot",
    "cdfFromBioC",
    "cdfFromEnvironment",
    "cdfFromLibPath",
    "cdfName",
    "checkValidFilenames",
    "cleancdfname",
    "close",
    "computeExprSet",
    "debug.affy123",
    "express.summary.stat",
    "express.summary.stat.methods",
    "expresso",
    "expressoWidget",
    "exprs",
    "exprs<-",
    "featureNames",
    "fit.li.wong",
    "geneNames",
    "generateExprSet.methods",
    "generateExprVal.method.avgdiff",
    "generateExprVal.method.liwong",
    "generateExprVal.method.mas",
    "generateExprVal.method.medianpolish",
    "generateExprVal.method.playerout",
    "getCdfInfo",
    "hist",
    "hlog",
    "image",
    "indexProbes",
    "indices2xy",
    "intensity",
    "intensity<-",
    "just.rma",
    "justRMA",
    "li.wong",
    "list.celfiles",
    "loess.normalize",
    "ma.plot",
    "maffy.normalize",
    "maffy.subset",
    "MAplot",
    "mas5",
    "mas5.detection",
    "mas5calls",
    "mas5calls.AffyBatch",
    "mas5calls.ProbeSet",
    "Mbox",
    "medianpolish",
    "merge.AffyBatch",
    "mm",
    "mm<-",
    "mmindex",
    "multiloess",
    "mva.pairs",
    "normalize.AffyBatch.constant",
    "normalize.AffyBatch.contrasts",
    "normalize.AffyBatch.invariantset",
    "normalize.AffyBatch.loess",
    "normalize.AffyBatch.methods",
    "normalize.AffyBatch.qspline",
    "normalize.AffyBatch.quantiles",
    "normalize.AffyBatch.quantiles.robust",
    "normalize.constant",
    "normalize.invariantset",
    "normalize.loess",
    "normalize.methods",
    "normalize.qspline",
    "open",
    "pairs.AffyBatch",
    "playerout.costfunction",
    "plot.ProbeSet",
    "plotAffyRNAdeg",
    "plotDensity",
    "plotDensity.AffyBatch",
    "plotLocation",
    "pm",
    "pm<-",
    "pmcorrect.mas",
    "pmcorrect.methods",
    "pmcorrect.pmonly",
    "pmcorrect.subtractmm",
    "pmindex",
    "ppset.ttest",
    "ppsetApply",
    "probeNames",
    "probes",
    "probeset",
    "read.affybatch",
    "read.probematrix",
    "ReadAffy",
    "rma",
    "sampleNames",
    "se.exprs",
    "show",
    "simplemultiLoess",
    "summaryAffyRNAdeg",
    "tukey.biweight",
    "tukeybiweight",
    "upDate.bgcorrect.methods",
    "upDate.express.summary.stat.methods",
    "upDate.generateExprSet.methods",
    "upDate.normalize.AffyBatch.methods",
    "upDate.pmcorrect.methods",
    "updateMe",
    "updateObject",
    "whatcdf",
    "xy2indices"
  ],
  "_datasets": [
    {
      "name": "cdfenv.example",
      "title": "Example cdfenv",
      "object": "cdfenv.example",
      "file": "cdfenv.example.rda",
      "class": [
        "environment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mapCdfName",
      "title": "Clean Affymetrix's CDF name",
      "object": "mapCdfName",
      "file": "mapCdfName.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "inCDF",
        "inCEL",
        "inBioC"
      ],
      "rows": 3,
      "table": true,
      "tojson": true
    },
    {
      "name": "SpikeIn",
      "title": "SpikeIn Experiment Data: ProbeSet Example",
      "object": "SpikeIn",
      "file": "SpikeIn.rda",
      "class": [
        "ProbeSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "setAffyOptions",
      "title": "~~function to set options ~~",
      "topics": [
        ".setAffyOptions"
      ]
    },
    {
      "page": "affy-deprecated",
      "title": "Deprecated functions in package 'affy'",
      "topics": [
        "loess.normalize",
        "maffy.normalize",
        "multiloess",
        "simplemultiLoess"
      ]
    },
    {
      "page": "affy-options",
      "title": "Options for the affy package",
      "topics": [
        "affy-options"
      ]
    },
    {
      "page": "affy.scalevalue.exprSet",
      "title": "Scale normalization for expreSets",
      "topics": [
        "affy.scalevalue.exprSet"
      ]
    },
    {
      "page": "AffyBatch-class",
      "title": "Class AffyBatch",
      "topics": [
        "$.AffyBatch",
        "AffyBatch",
        "AffyBatch,ANY",
        "AffyBatch-class",
        "bg.correct,AffyBatch,character-method",
        "boxplot,AffyBatch-method",
        "cdfName",
        "cdfName,AffyBatch-method",
        "checkValidFilenames",
        "col,AffyBatch-method",
        "computeExprSet,AffyBatch,character,character-method",
        "dim,AffyBatch-method",
        "exprs,AffyBatch-method",
        "exprs<-,AffyBatch,ANY-method",
        "featureNames,AffyBatch-method",
        "featureNames<-,AffyBatch-method",
        "geneNames",
        "geneNames,AffyBatch-method",
        "geneNames<-",
        "geneNames<-,AffyBatch,ANY-method",
        "getCdfInfo",
        "getCdfInfo,AffyBatch-method",
        "hist,AffyBatch-method",
        "image",
        "image,AffyBatch-method",
        "indexProbes",
        "indexProbes,AffyBatch,character-method",
        "indexProbes,AffyBatch,missing-method",
        "indexProbes,AffyBatch-method",
        "initialize,AffyBatch-method",
        "intensity",
        "intensity,AffyBatch-method",
        "intensity<-",
        "intensity<-,AffyBatch-method",
        "length,AffyBatch-method",
        "mm,AffyBatch-method",
        "mm<-,AffyBatch,ANY-method",
        "mmindex",
        "mmindex,AffyBatch-method",
        "pm,AffyBatch-method",
        "pm<-,AffyBatch,ANY-method",
        "pmindex",
        "pmindex,AffyBatch-method",
        "probeNames,AffyBatch-method",
        "probes",
        "probes,AffyBatch-method",
        "probeset",
        "probeset,AffyBatch-method",
        "row,AffyBatch-method",
        "se.exprs,AffyBatch-method",
        "se.exprs<-,AffyBatch-method",
        "show,AffyBatch-method",
        "updateObject,AffyBatch-method",
        "[,AffyBatch-method",
        "[<-,AffyBatch-method",
        "[[,AffyBatch-method"
      ]
    },
    {
      "page": "AffyRNAdeg",
      "title": "Function to assess RNA degradation in Affymetrix GeneChip data.",
      "topics": [
        "AffyRNAdeg",
        "plotAffyRNAdeg",
        "summaryAffyRNAdeg"
      ]
    },
    {
      "page": "barplot.ProbeSet",
      "title": "show a ProbeSet as barplots",
      "topics": [
        "barplot.ProbeSet"
      ]
    },
    {
      "page": "bg.adjust",
      "title": "Background adjustment (internal function)",
      "topics": [
        "bg.adjust",
        "bg.parameters"
      ]
    },
    {
      "page": "bgc",
      "title": "Background Correction",
      "topics": [
        "bg.correct",
        "bg.correct.mas",
        "bg.correct.none",
        "bg.correct.rma"
      ]
    },
    {
      "page": "cdfenv.example",
      "title": "Example cdfenv",
      "topics": [
        "cdfenv.example"
      ]
    },
    {
      "page": "cdfFromBioC",
      "title": "Functions to obtain CDF files",
      "topics": [
        "cdfFromBioC",
        "cdfFromEnvironment",
        "cdfFromLibPath"
      ]
    },
    {
      "page": "cleancdfname",
      "title": "Clean Affymetrix's CDF name",
      "topics": [
        "cleancdfname",
        "mapCdfName"
      ]
    },
    {
      "page": "debug.affy123",
      "title": "Debugging Flag",
      "topics": [
        "debug.affy123"
      ]
    },
    {
      "page": "expresso",
      "title": "From raw probe intensities to expression values",
      "topics": [
        "bgcorrect",
        "expresso"
      ]
    },
    {
      "page": "expressoWidget",
      "title": "A widget for users to pick correction methods",
      "topics": [
        "expressoWidget"
      ]
    },
    {
      "page": "fit.li.wong",
      "title": "Fit Li and Wong Model to a Probe Set",
      "topics": [
        "fit.li.wong",
        "li.wong"
      ]
    },
    {
      "page": "generateExprSet-methods",
      "title": "generate a set of expression values",
      "topics": [
        "computeExprSet",
        "generateExprSet-methods",
        "generateExprSet.methods",
        "upDate.generateExprSet.methods"
      ]
    },
    {
      "page": "generateExprVal-methods",
      "title": "Compute a summary expression value from the probes intensities",
      "topics": [
        "express.summary.stat",
        "express.summary.stat-methods",
        "express.summary.stat.methods",
        "upDate.express.summary.stat.methods"
      ]
    },
    {
      "page": "generateExprVal.method.avgdiff",
      "title": "Generate an expression value from the probes informations",
      "topics": [
        "generateExprVal.method.avgdiff",
        "generateExprVal.method.liwong",
        "generateExprVal.method.mas",
        "generateExprVal.method.medianpolish"
      ]
    },
    {
      "page": "generateExprVal.method.playerout",
      "title": "Generate an expression value from the probes informations",
      "topics": [
        "generateExprVal.method.playerout",
        "playerout.costfunction"
      ]
    },
    {
      "page": "hlog",
      "title": "Hybrid Log",
      "topics": [
        "hlog"
      ]
    },
    {
      "page": "justrma",
      "title": "Read CEL files into an ExpressionSet",
      "topics": [
        "just.rma",
        "justRMA"
      ]
    },
    {
      "page": "list.celfiles",
      "title": "List the Cel Files in a Directory/Folder",
      "topics": [
        "list.celfiles"
      ]
    },
    {
      "page": "MAplot",
      "title": "Relative M vs. A plots",
      "topics": [
        "ma.plot",
        "MAplot",
        "MAplot,AffyBatch-method",
        "Mbox",
        "Mbox,AffyBatch-method"
      ]
    },
    {
      "page": "mas5",
      "title": "MAS 5.0 expression measure",
      "topics": [
        "mas5"
      ]
    },
    {
      "page": "mas5calls",
      "title": "MAS 5.0 Absolute Detection",
      "topics": [
        "mas5.detection",
        "mas5calls",
        "mas5calls,AffyBatch-method",
        "mas5calls,ProbeSet-method",
        "mas5calls.AffyBatch",
        "mas5calls.ProbeSet"
      ]
    },
    {
      "page": "merge.AffyBatch",
      "title": "merge two AffyBatch objects",
      "topics": [
        "merge.AffyBatch"
      ]
    },
    {
      "page": "mva.pairs",
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