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  "Description": "A package that extends and improves the functionality of\nthe base affy package. Routines that make heavy use of compiled\ncode for speed. Central focus is on implementation of methods\nfor fitting probe-level models and tools using these models.\nPLM based quality assessment tools.",
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    "PLMset2exprSet",
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    "pset2eset",
    "pseudoColorBar",
    "pseudoPalette",
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    "resid<-",
    "residSE",
    "residuals<-",
    "RLE",
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    "se",
    "se.const",
    "se.probe",
    "se<-",
    "summary",
    "threestep",
    "threestepPLM",
    "varcov",
    "verify.bg.param",
    "verify.constraint.types",
    "verify.model.param",
    "verify.norm.param",
    "verify.output.param",
    "verify.variable.types",
    "weights<-"
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      ]
    },
    {
      "page": "fitPLM",
      "title": "Fit a Probe Level Model to Affymetrix Genechip Data.",
      "topics": [
        "fitPLM"
      ]
    },
    {
      "page": "MAplot",
      "title": "Relative M vs. A plots",
      "topics": [
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        "MAplot,PLMset-method"
      ]
    },
    {
      "page": "normalize.exprSet",
      "title": "Normalization applied to ExpressionSets",
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        "normalize.ExpressionSet.invariantset",
        "normalize.ExpressionSet.loess",
        "normalize.ExpressionSet.methods",
        "normalize.ExpressionSet.qspline",
        "normalize.ExpressionSet.quantiles",
        "normalize.ExpressionSet.scaling"
      ]
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      "topics": [
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      ]
    },
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      "title": "Scaling normalization",
      "topics": [
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        "normalize.scaling"
      ]
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      "title": "Class PLMset",
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        "boxplot,PLMset-method",
        "cdfName,PLMset-method",
        "coefs",
        "coefs,PLMset-method",
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        "coefs.probe",
        "coefs.probe,PLMset-method",
        "coefs<-",
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        "description,PLMset-method",
        "getCdfInfo,PLMset-method",
        "image,PLMset-method",
        "indexProbes,PLMset,character-method",
        "indexProbesProcessed",
        "indexProbesProcessed,PLMset-method",
        "Mbox",
        "Mbox,PLMset-method",
        "model.description",
        "model.description,PLMset-method",
        "normvec",
        "normvec,PLMset-method",
        "NUSE",
        "nuse",
        "NUSE,PLMset-method",
        "nuse,PLMset-method",
        "pData,PLMset-method",
        "pData<-,PLMset,data.frame-method",
        "phenoData,PLMset-method",
        "phenoData<-,PLMset,AnnotatedDataFrame-method",
        "PLMset",
        "PLMset-class",
        "resid",
        "resid,PLMset-method",
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        "resid<-,PLMset-method",
        "residSE",
        "residSE,PLMset-method",
        "residuals",
        "residuals,PLMset-method",
        "residuals<-",
        "residuals<-,PLMset-method",
        "RLE",
        "RLE,PLMset-method",
        "sampleNames,PLMset-method",
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        "sampleNames<-,PLMset,character-method",
        "se",
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        "se.const,PLMset-method",
        "se.probe",
        "se.probe,PLMset-method",
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