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<head><title>R: Linear Models for Microarray Data</title>
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<h1> Linear Models for Microarray Data
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</div><h2>Documentation for package ‘limma’ version 3.34.0</h2>
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<table width="100%">
<tr><td style="width: 25%;"><a href="01Introduction.html">limma-package</a></td>
<td>Introduction to the LIMMA Package</td></tr>
</table>
<h2><a name="A">-- A --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="alias2Symbol.html">alias2Symbol</a></td>
<td>Convert Gene Aliases to Official Gene Symbols</td></tr>
<tr><td style="width: 25%;"><a href="alias2Symbol.html">alias2SymbolTable</a></td>
<td>Convert Gene Aliases to Official Gene Symbols</td></tr>
<tr><td style="width: 25%;"><a href="alias2Symbol.html">alias2SymbolUsingNCBI</a></td>
<td>Convert Gene Aliases to Official Gene Symbols</td></tr>
<tr><td style="width: 25%;"><a href="anova-method.html">anova.MAList</a></td>
<td>ANOVA Table - method</td></tr>
<tr><td style="width: 25%;"><a href="targetsA2C.html">array2channel</a></td>
<td>Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel</td></tr>
<tr><td style="width: 25%;"><a href="arrayWeights.html">arrayWeights</a></td>
<td>Array Quality Weights</td></tr>
<tr><td style="width: 25%;"><a href="arrayWeightsQuick.html">arrayWeightsQuick</a></td>
<td>Array Quality Weights</td></tr>
<tr><td style="width: 25%;"><a href="arrayWeights.html">arrayWeightsSimple</a></td>
<td>Array Quality Weights</td></tr>
<tr><td style="width: 25%;"><a href="asdataframe.html">as.data.frame.EList</a></td>
<td>Turn a Microarray Linear Model Object into a Dataframe</td></tr>
<tr><td style="width: 25%;"><a href="asdataframe.html">as.data.frame.EListRaw</a></td>
<td>Turn a Microarray Linear Model Object into a Dataframe</td></tr>
<tr><td style="width: 25%;"><a href="asdataframe.html">as.data.frame.MAList</a></td>
<td>Turn a Microarray Linear Model Object into a Dataframe</td></tr>
<tr><td style="width: 25%;"><a href="asdataframe.html">as.data.frame.MArrayLM</a></td>
<td>Turn a Microarray Linear Model Object into a Dataframe</td></tr>
<tr><td style="width: 25%;"><a href="asmalist.html">as.MAList</a></td>
<td>Convert marrayNorm Object to an MAList Object</td></tr>
<tr><td style="width: 25%;"><a href="asmatrix.html">as.matrix.EList</a></td>
<td>Turn a Microarray Data Object into a Matrix</td></tr>
<tr><td style="width: 25%;"><a href="asmatrix.html">as.matrix.EListRaw</a></td>
<td>Turn a Microarray Data Object into a Matrix</td></tr>
<tr><td style="width: 25%;"><a href="asmatrix.html">as.matrix.ExpressionSet</a></td>
<td>Turn a Microarray Data Object into a Matrix</td></tr>
<tr><td style="width: 25%;"><a href="asmatrix.html">as.matrix.LumiBatch</a></td>
<td>Turn a Microarray Data Object into a Matrix</td></tr>
<tr><td style="width: 25%;"><a href="asmatrix.html">as.matrix.MAList</a></td>
<td>Turn a Microarray Data Object into a Matrix</td></tr>
<tr><td style="width: 25%;"><a href="asmatrix.html">as.matrix.MArrayLM</a></td>
<td>Turn a Microarray Data Object into a Matrix</td></tr>
<tr><td style="width: 25%;"><a href="asmatrix.html">as.matrix.marrayNorm</a></td>
<td>Turn a Microarray Data Object into a Matrix</td></tr>
<tr><td style="width: 25%;"><a href="asmatrix.html">as.matrix.PLMset</a></td>
<td>Turn a Microarray Data Object into a Matrix</td></tr>
<tr><td style="width: 25%;"><a href="asmatrix.html">as.matrix.RGList</a></td>
<td>Turn a Microarray Data Object into a Matrix</td></tr>
<tr><td style="width: 25%;"><a href="asmatrix.html">as.matrix.vsn</a></td>
<td>Turn a Microarray Data Object into a Matrix</td></tr>
<tr><td style="width: 25%;"><a href="asMatrixWeights.html">asMatrixWeights</a></td>
<td>asMatrixWeights</td></tr>
<tr><td style="width: 25%;"><a href="auROC.html">auROC</a></td>
<td>Area Under Receiver Operating Curve</td></tr>
<tr><td style="width: 25%;"><a href="avearrays.html">avearrays</a></td>
<td>Average Over Replicate Arrays</td></tr>
<tr><td style="width: 25%;"><a href="avearrays.html">avearrays.default</a></td>
<td>Average Over Replicate Arrays</td></tr>
<tr><td style="width: 25%;"><a href="avearrays.html">avearrays.EList</a></td>
<td>Average Over Replicate Arrays</td></tr>
<tr><td style="width: 25%;"><a href="avearrays.html">avearrays.MAList</a></td>
<td>Average Over Replicate Arrays</td></tr>
<tr><td style="width: 25%;"><a href="avedups.html">avedups</a></td>
<td>Average Over Duplicate Spots</td></tr>
<tr><td style="width: 25%;"><a href="avedups.html">avedups.default</a></td>
<td>Average Over Duplicate Spots</td></tr>
<tr><td style="width: 25%;"><a href="avedups.html">avedups.EList</a></td>
<td>Average Over Duplicate Spots</td></tr>
<tr><td style="width: 25%;"><a href="avedups.html">avedups.MAList</a></td>
<td>Average Over Duplicate Spots</td></tr>
<tr><td style="width: 25%;"><a href="avereps.html">avereps</a></td>
<td>Average Over Irregular Replicate Probes</td></tr>
<tr><td style="width: 25%;"><a href="avereps.html">avereps.default</a></td>
<td>Average Over Irregular Replicate Probes</td></tr>
<tr><td style="width: 25%;"><a href="avereps.html">avereps.EList</a></td>
<td>Average Over Irregular Replicate Probes</td></tr>
<tr><td style="width: 25%;"><a href="avereps.html">avereps.EListRaw</a></td>
<td>Average Over Irregular Replicate Probes</td></tr>
<tr><td style="width: 25%;"><a href="avereps.html">avereps.MAList</a></td>
<td>Average Over Irregular Replicate Probes</td></tr>
<tr><td style="width: 25%;"><a href="avereps.html">avereps.RGList</a></td>
<td>Average Over Irregular Replicate Probes</td></tr>
</table>
<h2><a name="B">-- B --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="backgroundcorrect.html">backgroundCorrect</a></td>
<td>Correct Intensities for Background</td></tr>
<tr><td style="width: 25%;"><a href="backgroundcorrect.html">backgroundCorrect.matrix</a></td>
<td>Correct Intensities for Background</td></tr>
<tr><td style="width: 25%;"><a href="barcodeplot.html">barcodeplot</a></td>
<td>Barcode Enrichment Plot</td></tr>
<tr><td style="width: 25%;"><a href="beadCountWeights.html">beadCountWeights</a></td>
<td>Bead Count Weights for Illumina BeadChips</td></tr>
<tr><td style="width: 25%;"><a href="blockDiag.html">blockDiag</a></td>
<td>Block Diagonal Matrix</td></tr>
<tr><td style="width: 25%;"><a href="bwss.html">bwss</a></td>
<td>Between and within sums of squares</td></tr>
<tr><td style="width: 25%;"><a href="bwss.matrix.html">bwss.matrix</a></td>
<td>Between and within sums of squares for matrix</td></tr>
</table>
<h2><a name="C">-- C --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="camera.html">camera</a></td>
<td>Competitive Gene Set Test Accounting for Inter-gene Correlation</td></tr>
<tr><td style="width: 25%;"><a href="camera.html">camera.default</a></td>
<td>Competitive Gene Set Test Accounting for Inter-gene Correlation</td></tr>
<tr><td style="width: 25%;"><a href="camera.html">cameraPR</a></td>
<td>Competitive Gene Set Test Accounting for Inter-gene Correlation</td></tr>
<tr><td style="width: 25%;"><a href="camera.html">cameraPR.default</a></td>
<td>Competitive Gene Set Test Accounting for Inter-gene Correlation</td></tr>
<tr><td style="width: 25%;"><a href="cbind.html">cbind</a></td>
<td>Combine RGList, MAList, EList or EListRaw Objects</td></tr>
<tr><td style="width: 25%;"><a href="cbind.html">cbind.EList</a></td>
<td>Combine RGList, MAList, EList or EListRaw Objects</td></tr>
<tr><td style="width: 25%;"><a href="cbind.html">cbind.EListRaw</a></td>
<td>Combine RGList, MAList, EList or EListRaw Objects</td></tr>
<tr><td style="width: 25%;"><a href="cbind.html">cbind.MAList</a></td>
<td>Combine RGList, MAList, EList or EListRaw Objects</td></tr>
<tr><td style="width: 25%;"><a href="cbind.html">cbind.RGList</a></td>
<td>Combine RGList, MAList, EList or EListRaw Objects</td></tr>
<tr><td style="width: 25%;"><a href="changelog.html">changeLog</a></td>
<td>Limma Change Log</td></tr>
<tr><td style="width: 25%;"><a href="classifytests.html">classifyTestsF</a></td>
<td>Multiple Testing Genewise Across Contrasts</td></tr>
<tr><td style="width: 25%;"><a href="classifytests.html">classifyTestsP</a></td>
<td>Multiple Testing Genewise Across Contrasts</td></tr>
<tr><td style="width: 25%;"><a href="classifytests.html">classifyTestsT</a></td>
<td>Multiple Testing Genewise Across Contrasts</td></tr>
<tr><td style="width: 25%;"><a href="rglist.html">coerce-method</a></td>
<td>Red, Green Intensity List - class</td></tr>
<tr><td style="width: 25%;"><a href="contrastAsCoef.html">contrastAsCoef</a></td>
<td>Reform a Design Matrix to that Contrasts Become Coefficients</td></tr>
<tr><td style="width: 25%;"><a href="contrasts.fit.html">contrasts.fit</a></td>
<td>Compute Contrasts from Linear Model Fit</td></tr>
<tr><td style="width: 25%;"><a href="controlStatus.html">controlStatus</a></td>
<td>Set Status of each Spot from List of Spot Types</td></tr>
<tr><td style="width: 25%;"><a href="propTrueNull.html">convest</a></td>
<td>Estimate Proportion of True Null Hypotheses</td></tr>
<tr><td style="width: 25%;"><a href="coolmap.html">coolmap</a></td>
<td>Heatmap of gene expression values</td></tr>
<tr><td style="width: 25%;"><a href="cumOverlap.html">cumOverlap</a></td>
<td>Cumulative Overlap Analysis of Ordered Lists</td></tr>
</table>
<h2><a name="D">-- D --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="decideTests.html">decideTests</a></td>
<td>Multiple Testing Across Genes and Contrasts</td></tr>
<tr><td style="width: 25%;"><a href="decideTests.html">decideTests.default</a></td>
<td>Multiple Testing Across Genes and Contrasts</td></tr>
<tr><td style="width: 25%;"><a href="decideTests.html">decideTests.MArrayLM</a></td>
<td>Multiple Testing Across Genes and Contrasts</td></tr>
<tr><td style="width: 25%;"><a href="channel2M.html">designI2A</a></td>
<td>Convert Individual Channel Design Matrix to M-A Format</td></tr>
<tr><td style="width: 25%;"><a href="channel2M.html">designI2M</a></td>
<td>Convert Individual Channel Design Matrix to M-A Format</td></tr>
<tr><td style="width: 25%;"><a href="detectionPValue.html">detectionPValues</a></td>
<td>Detection P-Values from Negative Controls</td></tr>
<tr><td style="width: 25%;"><a href="detectionPValue.html">detectionPValues.default</a></td>
<td>Detection P-Values from Negative Controls</td></tr>
<tr><td style="width: 25%;"><a href="detectionPValue.html">detectionPValues.EListRaw</a></td>
<td>Detection P-Values from Negative Controls</td></tr>
<tr><td style="width: 25%;"><a href="diffSplice.html">diffSplice</a></td>
<td>Test for Differential Splicing</td></tr>
<tr><td style="width: 25%;"><a href="dim.html">dim.EList</a></td>
<td>Retrieve the Dimensions of an RGList, MAList or MArrayLM Object</td></tr>
<tr><td style="width: 25%;"><a href="dim.html">dim.EListRaw</a></td>
<td>Retrieve the Dimensions of an RGList, MAList or MArrayLM Object</td></tr>
<tr><td style="width: 25%;"><a href="dim.html">dim.MAList</a></td>
<td>Retrieve the Dimensions of an RGList, MAList or MArrayLM Object</td></tr>
<tr><td style="width: 25%;"><a href="dim.html">dim.MArrayLM</a></td>
<td>Retrieve the Dimensions of an RGList, MAList or MArrayLM Object</td></tr>
<tr><td style="width: 25%;"><a href="dim.html">dim.RGList</a></td>
<td>Retrieve the Dimensions of an RGList, MAList or MArrayLM Object</td></tr>
<tr><td style="width: 25%;"><a href="dimnames.html">dimnames.EList</a></td>
<td>Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object</td></tr>
<tr><td style="width: 25%;"><a href="dimnames.html">dimnames.EListRaw</a></td>
<td>Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object</td></tr>
<tr><td style="width: 25%;"><a href="dimnames.html">dimnames.MAList</a></td>
<td>Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object</td></tr>
<tr><td style="width: 25%;"><a href="dimnames.html">dimnames.MArrayLM</a></td>
<td>Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object</td></tr>
<tr><td style="width: 25%;"><a href="dimnames.html">dimnames.RGList</a></td>
<td>Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object</td></tr>
<tr><td style="width: 25%;"><a href="dimnames.html">dimnames<-.EList</a></td>
<td>Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object</td></tr>
<tr><td style="width: 25%;"><a href="dimnames.html">dimnames<-.EListRaw</a></td>
<td>Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object</td></tr>
<tr><td style="width: 25%;"><a href="dimnames.html">dimnames<-.MAList</a></td>
<td>Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object</td></tr>
<tr><td style="width: 25%;"><a href="dimnames.html">dimnames<-.RGList</a></td>
<td>Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object</td></tr>
<tr><td style="width: 25%;"><a href="dupcor.html">duplicateCorrelation</a></td>
<td>Correlation Between Duplicates</td></tr>
</table>
<h2><a name="E">-- E --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="ebayes.html">eBayes</a></td>
<td>Empirical Bayes Statistics for Differential Expression</td></tr>
<tr><td style="width: 25%;"><a href="ebayes.html">ebayes</a></td>
<td>Empirical Bayes Statistics for Differential Expression</td></tr>
<tr><td style="width: 25%;"><a href="EList.html">EList-class</a></td>
<td>Expression List - class</td></tr>
<tr><td style="width: 25%;"><a href="EList.html">EListRaw-class</a></td>
<td>Expression List - class</td></tr>
<tr><td style="width: 25%;"><a href="propTrueNull.html">estimate.m0</a></td>
<td>Estimate Proportion of True Null Hypotheses</td></tr>
<tr><td style="width: 25%;"><a href="exprsMA.html">exprs.MA</a></td>
<td>Extract Log-Expression Matrix from MAList</td></tr>
</table>
<h2><a name="F">-- F --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="fitfdist.html">fitFDist</a></td>
<td>Moment Estimation of Scaled F-Distribution</td></tr>
<tr><td style="width: 25%;"><a href="fitfdist.html">fitFDistRobustly</a></td>
<td>Moment Estimation of Scaled F-Distribution</td></tr>
<tr><td style="width: 25%;"><a href="fitGammaIntercept.html">fitGammaIntercept</a></td>
<td>Fit Intercept to Vector of Gamma Distributed Variates</td></tr>
<tr><td style="width: 25%;"><a href="fitmixture.html">fitmixture</a></td>
<td>Fit Mixture Model by Non-Linear Least Squares</td></tr>
<tr><td style="width: 25%;"><a href="fitted.MArrayLM.html">fitted.MArrayLM</a></td>
<td>Fitted Values Method for MArrayLM Fits</td></tr>
<tr><td style="width: 25%;"><a href="roast.html">fry</a></td>
<td>Rotation Gene Set Tests</td></tr>
<tr><td style="width: 25%;"><a href="roast.html">fry.default</a></td>
<td>Rotation Gene Set Tests</td></tr>
<tr><td style="width: 25%;"><a href="classifytests.html">FStat</a></td>
<td>Multiple Testing Genewise Across Contrasts</td></tr>
</table>
<h2><a name="G">-- G --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="genas.html">genas</a></td>
<td>Genuine Association of Gene Expression Profiles</td></tr>
<tr><td style="width: 25%;"><a href="geneSetTest.html">geneSetTest</a></td>
<td>Mean-rank Gene Set Test</td></tr>
<tr><td style="width: 25%;"><a href="getlayout.html">getDupSpacing</a></td>
<td>Extract the Print Layout of an Array from the GAL File</td></tr>
<tr><td style="width: 25%;"><a href="getEAWP.html">getEAWP</a></td>
<td>Extract Basic Data from Expression Data Objects</td></tr>
<tr><td style="width: 25%;"><a href="goana.html">getGeneKEGGLinks</a></td>
<td>Gene Ontology or KEGG Pathway Analysis</td></tr>
<tr><td style="width: 25%;"><a href="goana.html">getKEGGPathwayNames</a></td>
<td>Gene Ontology or KEGG Pathway Analysis</td></tr>
<tr><td style="width: 25%;"><a href="getlayout.html">getLayout</a></td>
<td>Extract the Print Layout of an Array from the GAL File</td></tr>
<tr><td style="width: 25%;"><a href="getlayout.html">getLayout2</a></td>
<td>Extract the Print Layout of an Array from the GAL File</td></tr>
<tr><td style="width: 25%;"><a href="getSpacing.html">getSpacing</a></td>
<td>Get Numerical Spacing</td></tr>
<tr><td style="width: 25%;"><a href="gls.series.html">gls.series</a></td>
<td>Fit Linear Model to Microarray Data by Generalized Least Squares</td></tr>
<tr><td style="width: 25%;"><a href="goana.html">goana</a></td>
<td>Gene Ontology or KEGG Pathway Analysis</td></tr>
<tr><td style="width: 25%;"><a href="goana.html">goana.default</a></td>
<td>Gene Ontology or KEGG Pathway Analysis</td></tr>
<tr><td style="width: 25%;"><a href="goana.html">goana.MArrayLM</a></td>
<td>Gene Ontology or KEGG Pathway Analysis</td></tr>
<tr><td style="width: 25%;"><a href="gridspotrc.html">gridc</a></td>
<td>Row and Column Positions on Microarray</td></tr>
<tr><td style="width: 25%;"><a href="gridspotrc.html">gridr</a></td>
<td>Row and Column Positions on Microarray</td></tr>
</table>
<h2><a name="H">-- H --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="heatdiagram.html">heatDiagram</a></td>
<td>Stemmed Heat Diagram</td></tr>
<tr><td style="width: 25%;"><a href="heatdiagram.html">heatdiagram</a></td>
<td>Stemmed Heat Diagram</td></tr>
<tr><td style="width: 25%;"><a href="helpMethods.html">helpMethods</a></td>
<td>Prompt for Method Help Topics</td></tr>
</table>
<h2><a name="I">-- I --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="ids2indices.html">ids2indices</a></td>
<td>Convert Gene Identifiers to Indices for Gene Sets</td></tr>
<tr><td style="width: 25%;"><a href="imageplot.html">imageplot</a></td>
<td>Image Plot of Microarray Statistics</td></tr>
<tr><td style="width: 25%;"><a href="imageplot3by2.html">imageplot3by2</a></td>
<td>Write Imageplots to Files</td></tr>
<tr><td style="width: 25%;"><a href="camera.html">interGeneCorrelation</a></td>
<td>Competitive Gene Set Test Accounting for Inter-gene Correlation</td></tr>
<tr><td style="width: 25%;"><a href="intraspotCorrelation.html">intraspotCorrelation</a></td>
<td>Intra-Spot Correlation for Two Color Data</td></tr>
<tr><td style="width: 25%;"><a href="isfullrank.html">is.fullrank</a></td>
<td>Check for Full Column Rank</td></tr>
<tr><td style="width: 25%;"><a href="isnumeric.html">isNumeric</a></td>
<td>Test for Numeric Argument</td></tr>
</table>
<h2><a name="K">-- K --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="goana.html">kegga</a></td>
<td>Gene Ontology or KEGG Pathway Analysis</td></tr>
<tr><td style="width: 25%;"><a href="goana.html">kegga.default</a></td>
<td>Gene Ontology or KEGG Pathway Analysis</td></tr>
<tr><td style="width: 25%;"><a href="goana.html">kegga.MArrayLM</a></td>
<td>Gene Ontology or KEGG Pathway Analysis</td></tr>
<tr><td style="width: 25%;"><a href="kooperberg.html">kooperberg</a></td>
<td>Kooperberg Model-Based Background Correction for GenePix data</td></tr>
</table>
<h2><a name="L">-- L --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="LargeDataObject.html">LargeDataObject-class</a></td>
<td>Large Data Object - class</td></tr>
<tr><td style="width: 25%;"><a href="01Introduction.html">limma</a></td>
<td>Introduction to the LIMMA Package</td></tr>
<tr><td style="width: 25%;"><a href="limmaUsersGuide.html">limmaUsersGuide</a></td>
<td>View Limma User's Guide</td></tr>
<tr><td style="width: 25%;"><a href="lm.series.html">lm.series</a></td>
<td>Fit Linear Model to Microrray Data by Ordinary Least Squares</td></tr>
<tr><td style="width: 25%;"><a href="lmFit.html">lmFit</a></td>
<td>Linear Model for Series of Arrays</td></tr>
<tr><td style="width: 25%;"><a href="lmscFit.html">lmscFit</a></td>
<td>Fit Linear Model to Individual Channels of Two-Color Data</td></tr>
<tr><td style="width: 25%;"><a href="loessfit.html">loessFit</a></td>
<td>Univariate Lowess With Prior Weights</td></tr>
<tr><td style="width: 25%;"><a href="logcosh.html">logcosh</a></td>
<td>Logarithm of cosh</td></tr>
</table>
<h2><a name="M">-- M --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="normalizeWithinArrays.html">MA.RG</a></td>
<td>Normalize Within Arrays</td></tr>
<tr><td style="width: 25%;"><a href="ma3x3.html">ma3x3.matrix</a></td>
<td>Two dimensional Moving Averages with 3x3 Window</td></tr>
<tr><td style="width: 25%;"><a href="ma3x3.html">ma3x3.spottedarray</a></td>
<td>Two dimensional Moving Averages with 3x3 Window</td></tr>
<tr><td style="width: 25%;"><a href="makeContrasts.html">makeContrasts</a></td>
<td>Construct Matrix of Custom Contrasts</td></tr>
<tr><td style="width: 25%;"><a href="makeunique.html">makeUnique</a></td>
<td>Make Values of Character Vector Unique</td></tr>
<tr><td style="width: 25%;"><a href="malist.html">MAList-class</a></td>
<td>M-value, A-value Expression List - class</td></tr>
<tr><td style="width: 25%;"><a href="marraylm.html">MArrayLM-class</a></td>
<td>Microarray Linear Model Fit - class</td></tr>
<tr><td style="width: 25%;"><a href="mdplot.html">mdplot</a></td>
<td>Mean-Difference Plot</td></tr>
<tr><td style="width: 25%;"><a href="plotMDS.html">MDS-class</a></td>
<td>Multidimensional scaling plot of distances between gene expression profiles</td></tr>
<tr><td style="width: 25%;"><a href="merge.html">merge.EList</a></td>
<td>Merge RGList or MAList Data Objects</td></tr>
<tr><td style="width: 25%;"><a href="merge.html">merge.EListRaw</a></td>
<td>Merge RGList or MAList Data Objects</td></tr>
<tr><td style="width: 25%;"><a href="merge.html">merge.MAList</a></td>
<td>Merge RGList or MAList Data Objects</td></tr>
<tr><td style="width: 25%;"><a href="merge.html">merge.RGList</a></td>
<td>Merge RGList or MAList Data Objects</td></tr>
<tr><td style="width: 25%;"><a href="mergeScansRG.html">mergeScans</a></td>
<td>Merge two scans of two-color arrays</td></tr>
<tr><td style="width: 25%;"><a href="mergeScansRG.html">mergeScansRG</a></td>
<td>Merge two scans of two-color arrays</td></tr>
<tr><td style="width: 25%;"><a href="modelMatrix.html">modelMatrix</a></td>
<td>Construct Design Matrix</td></tr>
<tr><td style="width: 25%;"><a href="modifyWeights.html">modifyWeights</a></td>
<td>Modify Matrix of Weights By Control Status of Rows</td></tr>
<tr><td style="width: 25%;"><a href="mrlm.html">mrlm</a></td>
<td>Fit Linear Model to Microrray Data by Robust Regression</td></tr>
<tr><td style="width: 25%;"><a href="roast.html">mroast</a></td>
<td>Rotation Gene Set Tests</td></tr>
<tr><td style="width: 25%;"><a href="roast.html">mroast.default</a></td>
<td>Rotation Gene Set Tests</td></tr>
</table>
<h2><a name="N">-- N --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="nec.html">nec</a></td>
<td>NormExp Background Correction and Normalization Using Control Probes</td></tr>
<tr><td style="width: 25%;"><a href="nec.html">neqc</a></td>
<td>NormExp Background Correction and Normalization Using Control Probes</td></tr>
<tr><td style="width: 25%;"><a href="isfullrank.html">nonEstimable</a></td>
<td>Check for Full Column Rank</td></tr>
<tr><td style="width: 25%;"><a href="normalizebetweenarrays.html">normalizeBetweenArrays</a></td>
<td>Normalize Between Arrays</td></tr>
<tr><td style="width: 25%;"><a href="normalizeCyclicLoess.html">normalizeCyclicLoess</a></td>
<td>Normalize Columns of a Matrix by Cyclic Loess</td></tr>
<tr><td style="width: 25%;"><a href="normalizeprintorder.html">normalizeForPrintorder</a></td>
<td>Print-Order Normalization</td></tr>
<tr><td style="width: 25%;"><a href="normalizeprintorder.html">normalizeForPrintorder.rg</a></td>
<td>Print-Order Normalization</td></tr>
<tr><td style="width: 25%;"><a href="normalizeMedianAbsValues.html">normalizeMedianAbsValues</a></td>
<td>Normalize Columns of a Matrix to have the Median Absolute Value</td></tr>
<tr><td style="width: 25%;"><a href="normalizeMedianAbsValues.html">normalizeMedianValues</a></td>
<td>Normalize Columns of a Matrix to have the Median Absolute Value</td></tr>
<tr><td style="width: 25%;"><a href="normalizequantiles.html">normalizeQuantiles</a></td>
<td>Normalize Columns of a Matrix to have the same Quantiles</td></tr>
<tr><td style="width: 25%;"><a href="normalizeRobustSpline.html">normalizeRobustSpline</a></td>
<td>Normalize Single Microarray Using Shrunk Robust Splines</td></tr>
<tr><td style="width: 25%;"><a href="normalizeVSN.html">normalizeVSN</a></td>
<td>Variance Stabilizing Normalization (vsn)</td></tr>
<tr><td style="width: 25%;"><a href="normalizeVSN.html">normalizeVSN.default</a></td>
<td>Variance Stabilizing Normalization (vsn)</td></tr>
<tr><td style="width: 25%;"><a href="normalizeVSN.html">normalizeVSN.EListRaw</a></td>
<td>Variance Stabilizing Normalization (vsn)</td></tr>
<tr><td style="width: 25%;"><a href="normalizeVSN.html">normalizeVSN.RGList</a></td>
<td>Variance Stabilizing Normalization (vsn)</td></tr>
<tr><td style="width: 25%;"><a href="normalizeWithinArrays.html">normalizeWithinArrays</a></td>
<td>Normalize Within Arrays</td></tr>
<tr><td style="width: 25%;"><a href="normexpfit.html">normexp.fit</a></td>
<td>Fit Normal+Exp Convolution Model to Observed Intensities</td></tr>
<tr><td style="width: 25%;"><a href="normexpfitcontrol.html">normexp.fit.control</a></td>
<td>Normexp Model Parameter Estimation Aided by Negative Controls</td></tr>
<tr><td style="width: 25%;"><a href="normexpfitdetectionp.html">normexp.fit.detection.p</a></td>
<td>Estimate Normexp Model Parameter Using Negative Controls Inferred from Regular Probes</td></tr>
<tr><td style="width: 25%;"><a href="normexpsignal.html">normexp.signal</a></td>
<td>Expected Signal Given Observed Foreground Under Normal+Exp Model</td></tr>
</table>
<h2><a name="P">-- P --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="plotDensities.html">plotDensities</a></td>
<td>Plot Expression Densities</td></tr>
<tr><td style="width: 25%;"><a href="plotDensities.html">plotDensities.default</a></td>
<td>Plot Expression Densities</td></tr>
<tr><td style="width: 25%;"><a href="plotDensities.html">plotDensities.EList</a></td>
<td>Plot Expression Densities</td></tr>
<tr><td style="width: 25%;"><a href="plotDensities.html">plotDensities.EListRaw</a></td>
<td>Plot Expression Densities</td></tr>
<tr><td style="width: 25%;"><a href="plotDensities.html">plotDensities.MAList</a></td>
<td>Plot Expression Densities</td></tr>
<tr><td style="width: 25%;"><a href="plotDensities.html">plotDensities.RGList</a></td>
<td>Plot Expression Densities</td></tr>
<tr><td style="width: 25%;"><a href="plotExons.html">plotExons</a></td>
<td>Plot exons of differentially expressed gene</td></tr>
<tr><td style="width: 25%;"><a href="plotFB.html">plotFB</a></td>
<td>FB-Plot</td></tr>
<tr><td style="width: 25%;"><a href="plotFB.html">plotFB.default</a></td>
<td>FB-Plot</td></tr>
<tr><td style="width: 25%;"><a href="plotFB.html">plotFB.EListRaw</a></td>
<td>FB-Plot</td></tr>
<tr><td style="width: 25%;"><a href="plotFB.html">plotFB.RGList</a></td>
<td>FB-Plot</td></tr>
<tr><td style="width: 25%;"><a href="plotlines.html">plotlines</a></td>
<td>plotlines</td></tr>
<tr><td style="width: 25%;"><a href="plotma.html">plotMA</a></td>
<td>MA-Plot of Expression Data</td></tr>
<tr><td style="width: 25%;"><a href="plotma.html">plotMA.default</a></td>
<td>MA-Plot of Expression Data</td></tr>
<tr><td style="width: 25%;"><a href="plotma.html">plotMA.EList</a></td>
<td>MA-Plot of Expression Data</td></tr>
<tr><td style="width: 25%;"><a href="plotma.html">plotMA.EListRaw</a></td>
<td>MA-Plot of Expression Data</td></tr>
<tr><td style="width: 25%;"><a href="plotma.html">plotMA.MAList</a></td>
<td>MA-Plot of Expression Data</td></tr>
<tr><td style="width: 25%;"><a href="plotma.html">plotMA.MArrayLM</a></td>
<td>MA-Plot of Expression Data</td></tr>
<tr><td style="width: 25%;"><a href="plotma.html">plotMA.RGList</a></td>
<td>MA-Plot of Expression Data</td></tr>
<tr><td style="width: 25%;"><a href="plotma3by2.html">plotMA3by2</a></td>
<td>Write MA-Plots to Files</td></tr>
<tr><td style="width: 25%;"><a href="plotMD.html">plotMD</a></td>
<td>Mean-Difference Plot of Expression Data</td></tr>
<tr><td style="width: 25%;"><a href="plotMD.html">plotMD.default</a></td>
<td>Mean-Difference Plot of Expression Data</td></tr>
<tr><td style="width: 25%;"><a href="plotMD.html">plotMD.EList</a></td>
<td>Mean-Difference Plot of Expression Data</td></tr>
<tr><td style="width: 25%;"><a href="plotMD.html">plotMD.EListRaw</a></td>
<td>Mean-Difference Plot of Expression Data</td></tr>
<tr><td style="width: 25%;"><a href="plotMD.html">plotMD.MAList</a></td>
<td>Mean-Difference Plot of Expression Data</td></tr>
<tr><td style="width: 25%;"><a href="plotMD.html">plotMD.MArrayLM</a></td>
<td>Mean-Difference Plot of Expression Data</td></tr>
<tr><td style="width: 25%;"><a href="plotMD.html">plotMD.RGList</a></td>
<td>Mean-Difference Plot of Expression Data</td></tr>
<tr><td style="width: 25%;"><a href="plotMDS.html">plotMDS</a></td>
<td>Multidimensional scaling plot of distances between gene expression profiles</td></tr>
<tr><td style="width: 25%;"><a href="plotMDS.html">plotMDS.default</a></td>
<td>Multidimensional scaling plot of distances between gene expression profiles</td></tr>
<tr><td style="width: 25%;"><a href="plotMDS.html">plotMDS.MDS</a></td>
<td>Multidimensional scaling plot of distances between gene expression profiles</td></tr>
<tr><td style="width: 25%;"><a href="normalizeprintorder.html">plotPrintorder</a></td>
<td>Print-Order Normalization</td></tr>
<tr><td style="width: 25%;"><a href="plotprinttiploess.html">plotPrintTipLoess</a></td>
<td>MA Plots by Print-Tip Group</td></tr>
<tr><td style="width: 25%;"><a href="plotRLDF.html">plotRLDF</a></td>
<td>Plot of regularized linear discriminant functions for microarray data</td></tr>
<tr><td style="width: 25%;"><a href="plotSA.html">plotSA</a></td>
<td>Sigma vs A plot for microarray linear model</td></tr>
<tr><td style="width: 25%;"><a href="plotSplice.html">plotSplice</a></td>
<td>Differential splicing plot</td></tr>
<tr><td style="width: 25%;"><a href="plotWithHighlights.html">plotWithHighlights</a></td>
<td>Scatterplot With Highlighting of Special Points</td></tr>
<tr><td style="width: 25%;"><a href="poolvar.html">poolVar</a></td>
<td>Pool Sample Variances with Unequal Variances</td></tr>
<tr><td style="width: 25%;"><a href="predFCm.html">predFCm</a></td>
<td>Predictive log fold change for microarrays</td></tr>
<tr><td style="width: 25%;"><a href="printHead.html">printHead</a></td>
<td>Print Leading Rows of Large Objects</td></tr>
<tr><td style="width: 25%;"><a href="PrintLayout.html">PrintLayout-class</a></td>
<td>Print Layout - class</td></tr>
<tr><td style="width: 25%;"><a href="printorder.html">printorder</a></td>
<td>Identify Order in which Spots were Printed</td></tr>
<tr><td style="width: 25%;"><a href="printtipWeights.html">printtipWeights</a></td>
<td>Sub-array Quality Weights</td></tr>
<tr><td style="width: 25%;"><a href="printtipWeights.html">printtipWeightsSimple</a></td>
<td>Sub-array Quality Weights</td></tr>
<tr><td style="width: 25%;"><a href="propexpr.html">propexpr</a></td>
<td>Estimate Proportion of Expressed Probes</td></tr>
<tr><td style="width: 25%;"><a href="propTrueNull.html">propTrueNull</a></td>
<td>Estimate Proportion of True Null Hypotheses</td></tr>
<tr><td style="width: 25%;"><a href="protectMetachar.html">protectMetachar</a></td>
<td>Protect Metacharacters</td></tr>
</table>
<h2><a name="Q">-- Q --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="qqt.html">qqf</a></td>
<td>Student's t Quantile-Quantile Plot</td></tr>
<tr><td style="width: 25%;"><a href="qqt.html">qqt</a></td>
<td>Student's t Quantile-Quantile Plot</td></tr>
<tr><td style="width: 25%;"><a href="qualwt.html">QualityWeights</a></td>
<td>Spot Quality Weights</td></tr>
</table>
<h2><a name="R">-- R --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="rankSumTestwithCorrelation.html">rankSumTestWithCorrelation</a></td>
<td>Two Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For Correlation</td></tr>
<tr><td style="width: 25%;"><a href="cbind.html">rbind.EList</a></td>
<td>Combine RGList, MAList, EList or EListRaw Objects</td></tr>
<tr><td style="width: 25%;"><a href="cbind.html">rbind.EListRaw</a></td>
<td>Combine RGList, MAList, EList or EListRaw Objects</td></tr>
<tr><td style="width: 25%;"><a href="cbind.html">rbind.MAList</a></td>
<td>Combine RGList, MAList, EList or EListRaw Objects</td></tr>
<tr><td style="width: 25%;"><a href="cbind.html">rbind.RGList</a></td>
<td>Combine RGList, MAList, EList or EListRaw Objects</td></tr>
<tr><td style="width: 25%;"><a href="read.columns.html">read.columns</a></td>
<td>Read specified columns from a file</td></tr>
<tr><td style="width: 25%;"><a href="read.idat.html">read.idat</a></td>
<td>Read Illumina expression data directly from IDAT files</td></tr>
<tr><td style="width: 25%;"><a href="read.ilmn.html">read.ilmn</a></td>
<td>Read Illumina Expression Data</td></tr>
<tr><td style="width: 25%;"><a href="read.ilmn.targets.html">read.ilmn.targets</a></td>
<td>Read Illumina Data from a Target Dataframe</td></tr>
<tr><td style="width: 25%;"><a href="read.maimages.html">read.imagene</a></td>
<td>Read RGList or EListRaw from Image Analysis Output Files</td></tr>
<tr><td style="width: 25%;"><a href="read.maimages.html">read.maimages</a></td>
<td>Read RGList or EListRaw from Image Analysis Output Files</td></tr>
<tr><td style="width: 25%;"><a href="readgal.html">readGAL</a></td>
<td>Read a GAL file</td></tr>
<tr><td style="width: 25%;"><a href="readGPRHeader.html">readGenericHeader</a></td>
<td>Read Header Information from Microarray Raw Data File</td></tr>
<tr><td style="width: 25%;"><a href="readGPRHeader.html">readGPRHeader</a></td>
<td>Read Header Information from Microarray Raw Data File</td></tr>
<tr><td style="width: 25%;"><a href="readImaGeneHeader.html">readImaGeneHeader</a></td>
<td>Read ImaGene Header Information</td></tr>
<tr><td style="width: 25%;"><a href="readGPRHeader.html">readSMDHeader</a></td>
<td>Read Header Information from Microarray Raw Data File</td></tr>
<tr><td style="width: 25%;"><a href="readSpotTypes.html">readSpotTypes</a></td>
<td>Read Spot Types File</td></tr>
<tr><td style="width: 25%;"><a href="readTargets.html">readTargets</a></td>
<td>Read Targets File</td></tr>
<tr><td style="width: 25%;"><a href="removeBatchEffect.html">removeBatchEffect</a></td>
<td>Remove Batch Effect</td></tr>
<tr><td style="width: 25%;"><a href="removeext.html">removeExt</a></td>
<td>Remove Common Extension from File Names</td></tr>
<tr><td style="width: 25%;"><a href="residuals.MArrayLM.html">residuals.MArrayLM</a></td>
<td>Extract Residuals from MArrayLM Fit</td></tr>
<tr><td style="width: 25%;"><a href="normalizeWithinArrays.html">RG.MA</a></td>
<td>Normalize Within Arrays</td></tr>
<tr><td style="width: 25%;"><a href="rglist.html">RGList-class</a></td>
<td>Red, Green Intensity List - class</td></tr>
<tr><td style="width: 25%;"><a href="roast.html">roast</a></td>
<td>Rotation Gene Set Tests</td></tr>
<tr><td style="width: 25%;"><a href="roast.html">Roast-class</a></td>
<td>Rotation Gene Set Tests</td></tr>
<tr><td style="width: 25%;"><a href="roast.html">roast.default</a></td>
<td>Rotation Gene Set Tests</td></tr>
<tr><td style="width: 25%;"><a href="romer.html">romer</a></td>
<td>Rotation Gene Set Enrichment Analysis</td></tr>
<tr><td style="width: 25%;"><a href="romer.html">romer.default</a></td>
<td>Rotation Gene Set Enrichment Analysis</td></tr>
</table>
<h2><a name="S">-- S --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="selectmodel.html">selectModel</a></td>
<td>Select Appropriate Linear Model</td></tr>
<tr><td style="width: 25%;"><a href="LargeDataObject.html">show-method</a></td>
<td>Large Data Object - class</td></tr>
<tr><td style="width: 25%;"><a href="TestResults.html">show-method</a></td>
<td>Matrix of Test Results - class</td></tr>
<tr><td style="width: 25%;"><a href="plotMDS.html">show-method</a></td>
<td>Multidimensional scaling plot of distances between gene expression profiles</td></tr>
<tr><td style="width: 25%;"><a href="roast.html">show-method</a></td>
<td>Rotation Gene Set Tests</td></tr>
<tr><td style="width: 25%;"><a href="gridspotrc.html">spotc</a></td>
<td>Row and Column Positions on Microarray</td></tr>
<tr><td style="width: 25%;"><a href="gridspotrc.html">spotr</a></td>
<td>Row and Column Positions on Microarray</td></tr>
<tr><td style="width: 25%;"><a href="squeezeVar.html">squeezeVar</a></td>
<td>Squeeze Sample Variances</td></tr>
<tr><td style="width: 25%;"><a href="strsplit2.html">strsplit2</a></td>
<td>Split Composite Names</td></tr>
<tr><td style="width: 25%;"><a href="subsetting.html">subsetListOfArrays</a></td>
<td>Subset RGList, MAList, EListRaw, EList or MArrayLM Objects</td></tr>
<tr><td style="width: 25%;"><a href="subsetting.html">subsetting</a></td>
<td>Subset RGList, MAList, EListRaw, EList or MArrayLM Objects</td></tr>
<tr><td style="width: 25%;"><a href="summary.html">summary.EList</a></td>
<td>Summaries of Microarray Data Objects</td></tr>
<tr><td style="width: 25%;"><a href="summary.html">summary.EListRaw</a></td>
<td>Summaries of Microarray Data Objects</td></tr>
<tr><td style="width: 25%;"><a href="summary.html">summary.MAList</a></td>
<td>Summaries of Microarray Data Objects</td></tr>
<tr><td style="width: 25%;"><a href="summary.html">summary.MArrayLM</a></td>
<td>Summaries of Microarray Data Objects</td></tr>
<tr><td style="width: 25%;"><a href="summary.html">summary.RGList</a></td>
<td>Summaries of Microarray Data Objects</td></tr>
<tr><td style="width: 25%;"><a href="TestResults.html">summary.TestResults</a></td>
<td>Matrix of Test Results - class</td></tr>
</table>
<h2><a name="T">-- T --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="targetsA2C.html">targetsA2C</a></td>
<td>Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel</td></tr>
<tr><td style="width: 25%;"><a href="TestResults.html">TestResults-class</a></td>
<td>Matrix of Test Results - class</td></tr>
<tr><td style="width: 25%;"><a href="tmixture.html">tmixture.matrix</a></td>
<td>Estimate Scale Factor in Mixture of t-Distributions</td></tr>
<tr><td style="width: 25%;"><a href="tmixture.html">tmixture.vector</a></td>
<td>Estimate Scale Factor in Mixture of t-Distributions</td></tr>
<tr><td style="width: 25%;"><a href="topGO.html">topGO</a></td>
<td>Table of Top GO Terms or Top KEGG Pathways</td></tr>
<tr><td style="width: 25%;"><a href="topGO.html">topKEGG</a></td>
<td>Table of Top GO Terms or Top KEGG Pathways</td></tr>
<tr><td style="width: 25%;"><a href="topRomer.html">topRomer</a></td>
<td>Top Gene Set Testing Results from Romer</td></tr>
<tr><td style="width: 25%;"><a href="topSplice.html">topSplice</a></td>
<td>Top table of differentially spliced genes or exons</td></tr>
<tr><td style="width: 25%;"><a href="toptable.html">topTable</a></td>
<td>Table of Top Genes from Linear Model Fit</td></tr>
<tr><td style="width: 25%;"><a href="toptable.html">toptable</a></td>
<td>Table of Top Genes from Linear Model Fit</td></tr>
<tr><td style="width: 25%;"><a href="toptable.html">topTableF</a></td>
<td>Table of Top Genes from Linear Model Fit</td></tr>
<tr><td style="width: 25%;"><a href="toptable.html">topTreat</a></td>
<td>Table of Top Genes from Linear Model Fit</td></tr>
<tr><td style="width: 25%;"><a href="ebayes.html">treat</a></td>
<td>Empirical Bayes Statistics for Differential Expression</td></tr>
<tr><td style="width: 25%;"><a href="tricubeMovingAverage.html">tricubeMovingAverage</a></td>
<td>Moving Average Smoother With Tricube Weights</td></tr>
<tr><td style="width: 25%;"><a href="trigammainverse.html">trigammaInverse</a></td>
<td>Inverse Trigamma Function</td></tr>
<tr><td style="width: 25%;"><a href="trimWhiteSpace.html">trimWhiteSpace</a></td>
<td>Trim Leading and Trailing White Space</td></tr>
<tr><td style="width: 25%;"><a href="zscore.html">tZscore</a></td>
<td>Z-score Equivalents</td></tr>
</table>
<h2><a name="U">-- U --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="uniquegenelist.html">uniquegenelist</a></td>
<td>Eliminate Duplicate Names from the Gene List</td></tr>
<tr><td style="width: 25%;"><a href="modelMatrix.html">uniqueTargets</a></td>
<td>Construct Design Matrix</td></tr>
<tr><td style="width: 25%;"><a href="unwrapdups.html">unwrapdups</a></td>
<td>Unwrap Duplicate Spot Values from Rows into Columns</td></tr>
</table>
<h2><a name="V">-- V --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="venn.html">vennCounts</a></td>
<td>Venn Diagrams</td></tr>
<tr><td style="width: 25%;"><a href="venn.html">vennDiagram</a></td>
<td>Venn Diagrams</td></tr>
<tr><td style="width: 25%;"><a href="volcanoplot.html">volcanoplot</a></td>
<td>Volcano Plot</td></tr>
<tr><td style="width: 25%;"><a href="voom.html">voom</a></td>
<td>Transform RNA-Seq Data Ready for Linear Modelling</td></tr>
<tr><td style="width: 25%;"><a href="vooma.html">vooma</a></td>
<td>Convert Mean-Variance Trend to Observation-specific Precision Weights for Microarray Data</td></tr>
<tr><td style="width: 25%;"><a href="vooma.html">voomaByGroup</a></td>
<td>Convert Mean-Variance Trend to Observation-specific Precision Weights for Microarray Data</td></tr>
<tr><td style="width: 25%;"><a href="voomWithQualityWeights.html">voomWithQualityWeights</a></td>
<td>Combining observational-level with sample-specific quality weights for RNA-seq analysis</td></tr>
</table>
<h2><a name="W">-- W --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="weightedmedian.html">weighted.median</a></td>
<td>Weighted Median</td></tr>
<tr><td style="width: 25%;"><a href="weightedLowess.html">weightedLowess</a></td>
<td>Lowess fit with weighting</td></tr>
<tr><td style="width: 25%;"><a href="geneSetTest.html">wilcoxGST</a></td>
<td>Mean-rank Gene Set Test</td></tr>
<tr><td style="width: 25%;"><a href="writefit.html">write.fit</a></td>
<td>Write MArrayLM Object to a File</td></tr>
<tr><td style="width: 25%;"><a href="wsva.html">wsva</a></td>
<td>Weighted Surrogate Variable Analysis</td></tr>
<tr><td style="width: 25%;"><a href="qualwt.html">wtarea</a></td>
<td>Spot Quality Weights</td></tr>
<tr><td style="width: 25%;"><a href="qualwt.html">wtflags</a></td>
<td>Spot Quality Weights</td></tr>
<tr><td style="width: 25%;"><a href="qualwt.html">wtIgnore.Filter</a></td>
<td>Spot Quality Weights</td></tr>
</table>
<h2><a name="Z">-- Z --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="zscore.html">zscore</a></td>
<td>Z-score Equivalents</td></tr>
<tr><td style="width: 25%;"><a href="zscore.html">zscoreGamma</a></td>
<td>Z-score Equivalents</td></tr>
<tr><td style="width: 25%;"><a href="zscore.html">zscoreHyper</a></td>
<td>Z-score Equivalents</td></tr>
<tr><td style="width: 25%;"><a href="zscore.html">zscoreT</a></td>
<td>Z-score Equivalents</td></tr>
</table>
<h2><a name="misc">-- misc --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="01Introduction.html">01.Introduction</a></td>
<td>Introduction to the LIMMA Package</td></tr>
<tr><td style="width: 25%;"><a href="02classes.html">02.Classes</a></td>
<td>Topic: Classes Defined by this Package</td></tr>
<tr><td style="width: 25%;"><a href="03reading.html">03.ReadingData</a></td>
<td>Topic: Reading Microarray Data from Files</td></tr>
<tr><td style="width: 25%;"><a href="04Background.html">04.Background</a></td>
<td>Topic: Background Correction</td></tr>
<tr><td style="width: 25%;"><a href="05Normalization.html">05.Normalization</a></td>
<td>Topic: Normalization of Microarray Data</td></tr>
<tr><td style="width: 25%;"><a href="06linearmodels.html">06.LinearModels</a></td>
<td>Topic: Linear Models for Microarrays</td></tr>
<tr><td style="width: 25%;"><a href="07SingleChannel.html">07.SingleChannel</a></td>
<td>Topic: Individual Channel Analysis of Two-Color Microarrays</td></tr>
<tr><td style="width: 25%;"><a href="08Tests.html">08.Tests</a></td>
<td>Topic: Hypothesis Testing for Linear Models</td></tr>
<tr><td style="width: 25%;"><a href="09Diagnostics.html">09.Diagnostics</a></td>
<td>Topic: Diagnostics and Quality Assessment</td></tr>
<tr><td style="width: 25%;"><a href="10GeneSetTests.html">10.GeneSetTests</a></td>
<td>Topic: Gene Set Tests</td></tr>
<tr><td style="width: 25%;"><a href="11RNAseq.html">11.RNAseq</a></td>
<td>Topic: Analysis of RNA-seq Data</td></tr>
<tr><td style="width: 25%;"><a href="subsetting.html">[.EList</a></td>
<td>Subset RGList, MAList, EListRaw, EList or MArrayLM Objects</td></tr>
<tr><td style="width: 25%;"><a href="subsetting.html">[.EListRaw</a></td>
<td>Subset RGList, MAList, EListRaw, EList or MArrayLM Objects</td></tr>
<tr><td style="width: 25%;"><a href="subsetting.html">[.MAList</a></td>
<td>Subset RGList, MAList, EListRaw, EList or MArrayLM Objects</td></tr>
<tr><td style="width: 25%;"><a href="subsetting.html">[.MArrayLM</a></td>
<td>Subset RGList, MAList, EListRaw, EList or MArrayLM Objects</td></tr>
<tr><td style="width: 25%;"><a href="subsetting.html">[.RGList</a></td>
<td>Subset RGList, MAList, EListRaw, EList or MArrayLM Objects</td></tr>
</table>
</body></html>
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