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    "replicates",
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    "tTest",
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      "class": [
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      "fields": [],
      "table": false,
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      "page": "a4palette",
      "title": "Utility function that defines a color palette for use in a4",
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      ]
    },
    {
      "page": "addQuantilesColors",
      "title": "Compute quantiles for plotGeneDE function",
      "topics": [
        "addQuantilesColors"
      ]
    },
    {
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      "topics": [
        "boxPlot"
      ]
    },
    {
      "page": "combineTwoExpressionSet",
      "title": "Combine two ExpressionSet objects",
      "topics": [
        "combineTwoExpressionSet"
      ]
    },
    {
      "page": "computeLogRatio",
      "title": "Summary statistics for gene expression",
      "topics": [
        "computeLogRatio"
      ]
    },
    {
      "page": "createExpressionSet",
      "title": "combine gene expression and phenotype data onto a ExpressionSet object",
      "topics": [
        "createExpressionSet"
      ]
    },
    {
      "page": "ExpressionSetWithComputation-class",
      "title": "Class \"ExpressionSetWithComputation\"",
      "topics": [
        "ExpressionSetWithComputation-class"
      ]
    },
    {
      "page": "filterVarInt",
      "title": "Filtering on Intensity and Variance",
      "topics": [
        "filterVarInt"
      ]
    },
    {
      "page": "heatmap.expressionSet",
      "title": "Image plot of an expressionSet",
      "topics": [
        "heatmap.expressionSet"
      ]
    },
    {
      "page": "histPvalue",
      "title": "Plot the Distribution of P Values",
      "topics": [
        "histPvalue",
        "histPvalue,limma-method",
        "histPvalue,MArrayLM-method",
        "histPvalue,numeric-method"
      ]
    },
    {
      "page": "histpvalueplotter",
      "title": "Workhorse function for the histPvalue function",
      "topics": [
        "histpvalueplotter"
      ]
    },
    {
      "page": "lassoReg",
      "title": "Multiple regression using the Lasso algorithm as implemented in the glmnet package",
      "topics": [
        "lassoReg"
      ]
    },
    {
      "page": "limmaReg",
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        "limmaReg"
      ]
    },
    {
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      ]
    },
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      "title": "Logistic regression for predicting the probability to belong to a certain class in binary classification problems",
      "topics": [
        "logReg"
      ]
    },
    {
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      "title": "Data to Demonstrate nlcv and Co Functions",
      "topics": [
        "nlcvTT"
      ]
    },
    {
      "page": "oaColors",
      "title": "Pick One or More OA Colors",
      "topics": [
        "oaColors"
      ]
    },
    {
      "page": "oaPalette",
      "title": "Generate a Palette of OA Colors",
      "topics": [
        "oaPalette"
      ]
    },
    {
      "page": "plot1gene",
      "title": "Create a Profile Plot for a given Gene",
      "topics": [
        "plot1gene"
      ]
    },
    {
      "page": "plotComb2Samples",
      "title": "Plots the correlation in gene expression between two samples",
      "topics": [
        "plotComb2Samples"
      ]
    },
    {
      "page": "plotCombination2genes",
      "title": "Plot a Combination of Two Genes",
      "topics": [
        "plotCombination2genes"
      ]
    },
    {
      "page": "plotCombMultSamples",
      "title": "Plots the correlation in gene expression between more than 2 samples",
      "topics": [
        "plotCombMultSamples"
      ]
    },
    {
      "page": "plotLogRatio",
      "title": "Plot a summary gene expression graph",
      "topics": [
        "plotLogRatio"
      ]
    },
    {
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      "topics": [
        "probabilitiesPlot"
      ]
    },
    {
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      "title": "Translate Affymetrix probeset IDs into gene symbols",
      "topics": [
        "probe2gene"
      ]
    },
    {
      "page": "profilesPlot",
      "title": "Plot expression profiles of multiple genes or probesets Plot expression profiles of multiple genes or probesets. Each line depicts a gene, and the color legend can be used to identify the gene.",
      "topics": [
        "profilesPlot"
      ]
    },
    {
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      "title": "Generic function to compute the proportion of differentially expressed genes that are present",
      "topics": [
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      ]
    },
    {
      "page": "propDEgenes-methods",
      "title": "Generic function to compute the proportion of differentially expressed genes that are present",
      "topics": [
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        "propDEgenes,limma-method",
        "propDEgenes,numeric",
        "propDEgenes,numeric-method",
        "propDEgenes-methods"
      ]
    },
    {
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      "title": "Estimation of proportion of differentially expressed genes",
      "topics": [
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    },
    {
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      "topics": [
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    },
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      "topics": [
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    },
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        "spectralMap,ExpressionSet,character-method",
        "spectralMap-methods",
        "volcanoPlot,ExpressionSet,character"
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    },
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