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      "title": "Collinearity score",
      "topics": [
        "colinearityScore"
      ]
    },
    {
      "page": "deviation-method",
      "title": "Deviation from expectation for each observation",
      "topics": [
        "deviation",
        "deviation,MArrayLM-method"
      ]
    },
    {
      "page": "diffVar-method",
      "title": "Test differential variance",
      "topics": [
        "diffVar",
        "diffVar,MArrayLM-method"
      ]
    },
    {
      "page": "dream-method",
      "title": "Differential expression with linear mixed model",
      "topics": [
        "dream"
      ]
    },
    {
      "page": "dscchisq",
      "title": "Scaled chi-square",
      "topics": [
        "dscchisq"
      ]
    },
    {
      "page": "eBayes",
      "title": "eBayes generic for for MArrayLM and MArrayLM2",
      "topics": [
        "eBayes"
      ]
    },
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      "page": "eBayes-MArrayLM-method",
      "title": "eBayes for MArrayLM",
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    },
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      "page": "eBayes-method",
      "title": "eBayes for MArrayLM2",
      "topics": [
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      ]
    },
    {
      "page": "ESS-method",
      "title": "Effective sample size",
      "topics": [
        "ESS",
        "ESS,lmerMod-method"
      ]
    },
    {
      "page": "extractVarPart",
      "title": "Extract variance statistics",
      "topics": [
        "extractVarPart"
      ]
    },
    {
      "page": "fitExtractVarPartModel-method",
      "title": "Fit linear (mixed) model, report variance fractions",
      "topics": [
        "fitExtractVarPartModel",
        "fitExtractVarPartModel,data.frame-method",
        "fitExtractVarPartModel,EList-method",
        "fitExtractVarPartModel,ExpressionSet-method",
        "fitExtractVarPartModel,matrix-method",
        "fitExtractVarPartModel,sparseMatrix-method"
      ]
    },
    {
      "page": "fitVarPartModel-method",
      "title": "Fit linear (mixed) model",
      "topics": [
        "fitVarPartModel",
        "fitVarPartModel,data.frame-method",
        "fitVarPartModel,EList-method",
        "fitVarPartModel,ExpressionSet-method",
        "fitVarPartModel,matrix-method",
        "fitVarPartModel,sparseMatrix-method"
      ]
    },
    {
      "page": "get_prediction-method",
      "title": "Compute predicted value of formula for linear (mixed) model",
      "topics": [
        "get_prediction",
        "get_prediction,lm-method",
        "get_prediction,lmerMod-method"
      ]
    },
    {
      "page": "getContrast-method",
      "title": "Extract contrast matrix for linear mixed model",
      "topics": [
        "getContrast"
      ]
    },
    {
      "page": "getTreat-method",
      "title": "Test if coefficient is different from a specified value",
      "topics": [
        "getTreat",
        "getTreat,MArrayLM-method",
        "getTreat,MArrayLM2-method"
      ]
    },
    {
      "page": "ggColorHue",
      "title": "Default colors for ggplot",
      "topics": [
        "ggColorHue"
      ]
    },
    {
      "page": "hatvalues-method",
      "title": "Compute hatvalues",
      "topics": [
        "hatvalues,MArrayLM-method",
        "hatvalues,MArrayLM2-method"
      ]
    },
    {
      "page": "isRunableFormula",
      "title": "Test if formula is full rank on this dataset",
      "topics": [
        "isRunableFormula"
      ]
    },
    {
      "page": "logLik.MArrayLM",
      "title": "Log-likelihood from model fit",
      "topics": [
        "logLik.MArrayLM"
      ]
    },
    {
      "page": "logLik.MArrayLM2",
      "title": "Log-likelihood from model fit",
      "topics": [
        "logLik.MArrayLM2"
      ]
    },
    {
      "page": "makeContrastsDream",
      "title": "Construct Matrix of Custom Contrasts",
      "topics": [
        "makeContrastsDream"
      ]
    },
    {
      "page": "MArrayLM2-class",
      "title": "Class MArrayLM2",
      "topics": [
        "MArrayLM2-class"
      ]
    },
    {
      "page": "mvTest-method",
      "title": "Multivariate tests on results from 'dream()'",
      "topics": [
        "mvTest",
        "mvTest,MArrayLM,EList,integer-method",
        "mvTest,MArrayLM,EList,list-method",
        "mvTest,MArrayLM,EList,missing-method",
        "mvTest,MArrayLM,EList,vector-method",
        "mvTest,MArrayLM,matrix,ANY-method",
        "mvTest,MArrayLM,matrix-method",
        "mvTest,mvTest_input,ANY,ANY-method",
        "mvTest,mvTest_input,method"
      ]
    },
    {
      "page": "mvTest_input-class",
      "title": "Class mvTest_input",
      "topics": [
        "mvTest_input-class"
      ]
    },
    {
      "page": "plotCompareP-method",
      "title": "Compare p-values from two analyses",
      "topics": [
        "plotCompareP"
      ]
    },
    {
      "page": "plotContrasts",
      "title": "Plot representation of contrast matrix",
      "topics": [
        "plotContrasts"
      ]
    },
    {
      "page": "plotCorrMatrix",
      "title": "plotCorrMatrix",
      "topics": [
        "plotCorrMatrix"
      ]
    },
    {
      "page": "plotCorrStructure",
      "title": "plotCorrStructure",
      "topics": [
        "plotCorrStructure"
      ]
    },
    {
      "page": "plotPercentBars-method",
      "title": "Bar plot of gene fractions",
      "topics": [
        "plotPercentBars",
        "plotPercentBars,data.frame-method",
        "plotPercentBars,matrix-method",
        "plotPercentBars,varPartResults-method"
      ]
    },
    {
      "page": "plotStratify",
      "title": "plotStratify",
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        "plotStratify"
      ]
    },
    {
      "page": "plotStratifyBy",
      "title": "plotStratifyBy",
      "topics": [
        "plotStratifyBy"
      ]
    },
    {
      "page": "plotVarianceEstimates",
      "title": "Plot Variance Estimates",
      "topics": [
        "plotVarianceEstimates"
      ]
    },
    {
      "page": "plotVarPart-method",
      "title": "Violin plot of variance fractions",
      "topics": [
        "plotVarPart",
        "plotVarPart,data.frame-method",
        "plotVarPart,matrix-method",
        "plotVarPart,varPartResults-method"
      ]
    },
    {
      "page": "rdf",
      "title": "Residual degrees of freedom",
      "topics": [
        "rdf"
      ]
    },
    {
      "page": "rdf_from_matrices",
      "title": "Fast approximate residual degrees of freedom",
      "topics": [
        "rdf_from_matrices"
      ]
    },
    {
      "page": "rdf.merMod",
      "title": "Approximate residual degrees of freedom",
      "topics": [
        "rdf.merMod"
      ]
    },
    {
      "page": "reOnly",
      "title": "Adapted from lme4:::reOnly",
      "topics": [
        "reOnly"
      ]
    },
    {
      "page": "residuals-MArrayLM-method",
      "title": "residuals for MArrayLM",
      "topics": [
        "residuals,MArrayLM-method"
      ]
    },
    {
      "page": "residuals-MArrayLM2-method",
      "title": "residuals for MArrayLM2",
      "topics": [
        "residuals,MArrayLM2-method"
      ]
    },
    {
      "page": "residuals-VarParFitList-method",
      "title": "Residuals from model fit",
      "topics": [
        "residuals,VarParFitList-method"
      ]
    },
    {
      "page": "residuals.MArrayLM2",
      "title": "Residuals for result of dream",
      "topics": [
        "residuals.MArrayLM2"
      ]
    },
    {
      "page": "shrinkageMetric",
      "title": "Shrinkage metric for eBayes",
      "topics": [
        "shrinkageMetric"
      ]
    },
    {
      "page": "sortCols-method",
      "title": "Sort variance partition statistics",
      "topics": [
        "sortCols",
        "sortCols,data.frame-method",
        "sortCols,matrix-method",
        "sortCols,varPartResults-method"
      ]
    },
    {
      "page": "toptable-method",
      "title": "Table of Top Genes from Linear Model Fit",
      "topics": [
        "topTable",
        "topTable,MArrayLM-method",
        "toptable,MArrayLM-method",
        "topTable,MArrayLM2-method",
        "toptable,MArrayLM2-method"
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    },
    {
      "page": "VarParCIList-class",
      "title": "Class VarParCIList",
      "topics": [
        "VarParCIList-class"
      ]
    },
    {
      "page": "VarParFitList-class",
      "title": "Class VarParFitList",
      "topics": [
        "VarParFitList-class"
      ]
    },
    {
      "page": "varParFrac-class",
      "title": "Class varParFrac",
      "topics": [
        "varParFrac-class"
      ]
    },
    {
      "page": "varPartConfInf",
      "title": "Linear mixed model confidence intervals",
      "topics": [
        "varPartConfInf"
      ]
    },
    {
      "page": "varPartData",
      "title": "Simulation dataset for examples",
      "topics": [
        "geneCounts",
        "geneExpr",
        "info",
        "varPartData"
      ]
    },
    {
      "page": "varPartDEdata",
      "title": "A simulated dataset of gene counts",
      "topics": [
        "countMatrix",
        "metadata",
        "varPartDEdata"
      ]
    },
    {
      "page": "varPartResults-class",
      "title": "Class varPartResults",
      "topics": [
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      ]
    },
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      "page": "vcov-MArrayLM-method",
      "title": "Co-variance matrix for 'dream()' fit",
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      "page": "vcov-MArrayLM2-method",
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      "topics": [
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    },
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      "page": "vcovSqrt-method",
      "title": "Sqrt of co-variance matrix for 'dream()' fit",
      "topics": [
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        "mvTest,MArrayLM2-method",
        "vcovSqrt",
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    },
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      "page": "voomWithDreamWeights",
      "title": "Transform RNA-Seq Data Ready for Linear Mixed Modelling with 'dream()'",
      "topics": [
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        "Advanced analysis",
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