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  "Title": "Reads, Annotates, and Normalizes Reverse Phase Protein Array\nData",
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  "Author": "Heiko Mannsperger with contributions of Stephan Gade",
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    "dataPreproc",
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    "plotQC",
    "plotqq",
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    "rppaList2Heatmap",
    "sample.median",
    "select.measurements",
    "select.sample.group",
    "simpleBoxplot",
    "test.correlation",
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      "name": "dataI",
      "title": "Reverse phase protein array rawdata, samples serially diluted",
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      "table": false,
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      "tojson": true
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      "fields": [],
      "table": false,
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      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
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      "table": true,
      "tojson": true
    },
    {
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      "title": "Reverse phase protein array rawdata, samples serially diluted",
      "object": "ser.dil.samples",
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      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
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        "incubation_run",
        "target",
        "AB_ID",
        "spotted_volume"
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      "table": true,
      "tojson": true
    }
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  "_help": [
    {
      "page": "rppanalyzer-package",
      "title": "Read, annotate and normalize reverse phase protein array data and get a brief overview on the biological impact.",
      "topics": [
        "RPPanalyzer-package",
        "RPPanalyzer"
      ]
    },
    {
      "page": "averageData",
      "title": "Average biological replicates over different slides.",
      "topics": [
        "averageData"
      ]
    },
    {
      "page": "calcLinear",
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      "topics": [
        "calcLinear"
      ]
    },
    {
      "page": "calcLogistic",
      "title": "Calculates sample concentrations using sigmoid model fit",
      "topics": [
        "calcLogistic"
      ]
    },
    {
      "page": "calcSdc",
      "title": "Calculates the concentration of serial diluted samples",
      "topics": [
        "calcSdc"
      ]
    },
    {
      "page": "correctBG",
      "title": "Corrects for background in an RPPA data set",
      "topics": [
        "correctBG"
      ]
    },
    {
      "page": "correctDilinterc",
      "title": "Dilution series intersect correction",
      "topics": [
        "analyzeIntercepts",
        "as.my",
        "correctDilinterc",
        "getIntercepts",
        "getSignals"
      ]
    },
    {
      "page": "curvePredictSigmoid",
      "title": "Sigmoidal curve prediction.",
      "topics": [
        "curvePredictSigmoid"
      ]
    },
    {
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      "title": "Reverse phase protein array rawdata, samples serially diluted",
      "topics": [
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      ]
    },
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      "page": "dataII",
      "title": "Reverse phase protein array data, samples from a stimulation time course",
      "topics": [
        "dataII"
      ]
    },
    {
      "page": "dataIII",
      "title": "Reverse phase protein array data from original cancer specimen",
      "topics": [
        "dataIII"
      ]
    },
    {
      "page": "dataPreproc",
      "title": "Data preprocessing",
      "topics": [
        "dataPreproc"
      ]
    },
    {
      "page": "getErrorModel",
      "title": "Estimates error model parameters var0 (basal variance) and varR (relative variance) and produces a new data.frame with the signals and error model parameters.",
      "topics": [
        "getErrorModel"
      ]
    },
    {
      "page": "HKdata",
      "title": "Reverse phase protein array data of siRNA transfected cell line",
      "topics": [
        "HKdata"
      ]
    },
    {
      "page": "logList",
      "title": "Logarithmize (log2) the first two RPPA list elements, i.e. foreground and background signal intensities",
      "topics": [
        "logList"
      ]
    },
    {
      "page": "normalizeRPPA",
      "title": "Normalizes data in an RPPA data list",
      "topics": [
        "normalizeRPPA"
      ]
    },
    {
      "page": "pick.high.conc",
      "title": "Select the highest concentration from serialy diluted samples",
      "topics": [
        "pick.high.conc"
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    },
    {
      "page": "plotMeasurementsQC",
      "title": "Scatter Plots from an RPPA data",
      "topics": [
        "plotMeasurementsQC"
      ]
    },
    {
      "page": "plotQC",
      "title": "Plot target and blank signal from RPPA control samples",
      "topics": [
        "plotQC"
      ]
    },
    {
      "page": "plotqq",
      "title": "qq-plot and qq-line of an RPPA data set",
      "topics": [
        "plotqq"
      ]
    },
    {
      "page": "plotTimeCourse",
      "title": "Draw time course from RPPA data",
      "topics": [
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      ]
    },
    {
      "page": "plotTimeCourseII",
      "title": "Multiplot function for RPPA time course datasets",
      "topics": [
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    },
    {
      "page": "read.Data",
      "title": "Read and Annotate RPPA rawdata",
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      ]
    },
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      "title": "Remove arrays from a RPPA data list",
      "topics": [
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    {
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    {
      "page": "rppaList2ExpressionSet",
      "title": "Convert RPPA data into Expression Set",
      "topics": [
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      ]
    },
    {
      "page": "rppaList2Heatmap",
      "title": "Draw a heatmap with column side colors from a RPPA data",
      "topics": [
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    },
    {
      "page": "S1.gpr",
      "title": "GenePix result files",
      "topics": [
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    {
      "page": "sample.median",
      "title": "Aggregate the replicates in an RPPA data set",
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    {
      "page": "select.measurements",
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      "topics": [
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      "page": "simpleBoxplot",
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