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A B C D E F G H I K L M N P Q R S T U V W Z misc
| 1.Introduction | Introduction to the LIMMA Package |
| 2.Classes | Classes Defined by this Package |
| 3.ReadingData | Reading Microarray Data from Files |
| 4.Normalization | Normalization of Microarray Data |
| 5.LinearModels | Linear Models for Microarrays |
| 6.SingleChannel | Individual Channel Analysis of Two-Color Microarrays |
| 7.Diagnostics | Diagnostics and Quality Assessment |
| 8.Other | Other Functions |
| a.spot | Extract M or A-values from SPOT data.frame or matrix |
| anova.MAList | ANOVA Table - method |
| array2channel | Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel |
| arrayWeights | Array Quality Weights |
| arrayWeightsQuick | Array Quality Weights |
| as.data.frame.MArrayLM | Turn a Microarray Linear Model Object into a Dataframe |
| as.MAList | Convert marrayNorm Object to an MAList Object |
| as.matrix.exprSet | Turn a Microarray Data Object into a Matrix |
| as.matrix.MAList | Turn a Microarray Data Object into a Matrix |
| as.matrix.MArrayLM | Turn a Microarray Data Object into a Matrix |
| as.matrix.marrayNorm | Turn a Microarray Data Object into a Matrix |
| as.matrix.RGList | Turn a Microarray Data Object into a Matrix |
| auROC | Area Under Receiver Operating Curve |
| backgroundCorrect | Correct Intensities for Background |
| blockDiag | Block Diagonal Matrix |
| bwss | Between and within sums of squares |
| bwss.matrix | Between and within sums of squares for matrix |
| cbind.MAList | Combine RGList or MAList Objects |
| cbind.RGList | Combine RGList or MAList Objects |
| changeLog | Limma Change Log |
| classifyTests | Treat Simultaneous T-Tests as Classification Problem |
| classifyTestsF | Treat Simultaneous T-Tests as Classification Problem |
| classifyTestsP | Treat Simultaneous T-Tests as Classification Problem |
| classifyTestsT | Treat Simultaneous T-Tests as Classification Problem |
| coerce,RGList,exprSet2-method | Red, Green Intensity List - class |
| contrasts.fit | Compute Contrasts from Linear Model Fit |
| controlStatus | Set Status of each Spot from List of Spot Types |
| convest | Estimate Proportion of True Null Hypotheses |
| decideTests | Compute Matrix of Hypothesis Test Results |
| designI2A | Convert Individual Channel Design Matrix to M-A Format |
| designI2M | Convert Individual Channel Design Matrix to M-A Format |
| designMatrix | Construct Design Matrix |
| dim.MAList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
| dim.MArrayLM | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
| dim.RGList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
| dimnames.MAList | Retrieve the Dimension Names of an RGList, MAList or MArrayLM Object |
| dimnames.MArrayLM | Retrieve the Dimension Names of an RGList, MAList or MArrayLM Object |
| dimnames.RGList | Retrieve the Dimension Names of an RGList, MAList or MArrayLM Object |
| dupcor.series | Correlation Between Duplicates |
| duplicateCorrelation | Correlation Between Duplicates |
| eBayes | Empirical Bayes Statistics for Differential Expression |
| ebayes | Empirical Bayes Statistics for Differential Expression |
| exprSet2-class | Expression Set - class |
| fit.normexp | Fit Normal+Exp Convolution Model to Observed Intensities |
| fit.normexp0 | Fit Normal+Exp Convolution Model to Observed Intensities |
| fitFDist | Moment Estimation of Scaled F-Distribution |
| FStat | Treat Simultaneous T-Tests as Classification Problem |
| geneSetTest | Gene Set Test |
| getLayout | Extract the Print Layout of an Array from the GAL File |
| getLayout2 | Extract the Print Layout of an Array from the GAL File |
| getSpacing | Get Numerical Spacing |
| gls.series | Generalized Least Squares for Series of Microarrays |
| gridc | Row and Column Positions on Microarray |
| gridr | Row and Column Positions on Microarray |
| grloglik | Normal + Exponential Log-Likelihood |
| grsumloglik | Normal + Exponential Log-Likelihood |
| heatDiagram | Stemmed Heat Diagram |
| heatdiagram | Stemmed Heat Diagram |
| helpMethods | Prompt for Method Help Topics |
| imageplot | Image Plot of Microarray Statistics |
| imageplot3by2 | Write Imageplots to Files |
| intraspotCorrelation | Intra-Spot Correlation for Two Color Data |
| is.fullrank | Check for Full Column Rank |
| isNumeric | Test for Numeric Argument |
| kooperberg | Kooperberg Model-Based Background Correction |
| LargeDataObject-class | Large Data Object - class |
| length.MAList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
| length.MArrayLM | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
| length.RGList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
| limmaUsersGuide | View Limma User's Guide |
| lm.series | Linear Model for Series of Arrays |
| lmFit | Linear Model for Series of Arrays |
| lmscFit | Fit Linear Model to Individual Channels of Two-Color Data |
| loessFit | Fast Simple Loess |
| m.spot | Extract M or A-values from SPOT data.frame or matrix |
| m2loglik.normexp | Normal + Exponential Log-Likelihood |
| MA.RG | Normalize Within Arrays |
| ma3x3.matrix | Two dimensional Moving Averages with 3x3 Window |
| ma3x3.spottedarray | Two dimensional Moving Averages with 3x3 Window |
| makeContrasts | Construct Matrix of Custom Contrasts |
| makeUnique | Make Values of Character Vector Unique |
| MAList-class | M-value, A-value Expression List - class |
| MArrayLM-class | Microarray Linear Model Fit - class |
| matvec | Multiply a Matrix by a Vector |
| mdplot | mdplot |
| merge.MAList | Merge RGList or MAList Data Objects |
| merge.RGList | Merge RGList or MAList Data Objects |
| modelMatrix | Construct Design Matrix |
| modifyWeights | modifyWeights |
| mrlm | Robust Linear Model for Series of Microarrays |
| nonEstimable | Check for Full Column Rank |
| normalizeBetweenArrays | Normalize Between Arrays |
| normalizeForPrintorder | Print-Order Normalization |
| normalizeMedianDeviations | Normalize Columns of a Matrix to have the Same Scale |
| normalizeMedians | Normalize Columns of a Matrix to have the Same Scale |
| normalizeQuantiles | Normalize Columns of a Matrix to have the same Quantiles |
| normalizeRobustSpline | Normalize Single Microarray Using Shrunk Robust Splines |
| normalizeWithinArrays | Normalize Within Arrays |
| plotDensities | Individual-channel Densities Plot |
| plotMA | MA-Plot |
| plotMA3by2 | Write MA-Plots to Files |
| plotPrintorder | Print-Order Normalization |
| plotPrintTipLoess | MA Plots by Print-Tip Group |
| poolVar | Pool Sample Variances with Unequal Variances |
| printHead | Print Leading Rows of Large Objects |
| PrintLayout-class | Print Layout - class |
| printorder | Identify Order in which Spots were Printed |
| protectMetachar | Protect Metacharacters |
| qqt | Student's t Quantile-Quantile Plot |
| QualityWeights | Spot Quality Weights |
| rbind.MAList | Combine RGList or MAList Objects |
| rbind.RGList | Combine RGList or MAList Objects |
| read.imagene | Read RGList from Image Analysis Output Files |
| read.maimages | Read RGList from Image Analysis Output Files |
| read.matrix | Read Matrix with Headers from File |
| read.series | Read series of image files |
| readGAL | Read a GAL file |
| readGPRHeader | Read Header Information from Image Analysis Raw Data File |
| readImaGeneHeader | Read ImaGene Header Information |
| readSMDHeader | Read Header Information from Image Analysis Raw Data File |
| readSpotTypes | Read Spot Types File |
| readTargets | Read Targets File |
| removeExt | Remove Common Extension from File Names |
| rg.genepix | Extract RGList from data.frames Containing GenePix Data |
| RG.MA | Normalize Within Arrays |
| rg.quantarray | Extract RGList from data.frames Containing Quantarray Data |
| rg.series.spot | Read RGList from SPOT Image Analysis Output Files |
| rg.spot | Extract RGList from data.frames Containing SPOT Data |
| RGList-class | Red, Green Intensity List - class |
| rlm.series | Robust Linear Model for Series of Microarrays |
| show,LargeDataObject-method | Large Data Object - class |
| show,TestResults-method | Matrix of Test Results - class |
| signal.normexp | Expected Signal Given Observed Foreground Under Normal+Exp Model |
| splitName | Split Composite Gene Names |
| spotc | Row and Column Positions on Microarray |
| spotr | Row and Column Positions on Microarray |
| squeezeVar | Smooth Sample Variances |
| sumloglik | Normal + Exponential Log-Likelihood |
| summary.MAList | Summaries of Microarray Data Objects |
| summary.MArrayLM | Summaries of Microarray Data Objects |
| summary.RGList | Summaries of Microarray Data Objects |
| summary.TestResults | Matrix of Test Results - class |
| targetsA2C | Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel |
| TestResults-class | Matrix of Test Results - class |
| tmixture.matrix | Estimate Scale Factor in Mixture of t-Distributions |
| tmixture.vector | Estimate Scale Factor in Mixture of t-Distributions |
| topTable | Table of Top Genes from Linear Model Fit |
| toptable | Table of Top Genes from Linear Model Fit |
| trigammaInverse | Inverse Trigamma Function |
| trimWhiteSpace | Trim Leading and Trailing White Space |
| tZscore | z-score equivalents |
| uniquegenelist | Eliminate Duplicate Names from the Gene List |
| uniqueTargets | Construct Design Matrix |
| unwrapdups | Unwrap Duplicate Spot Values from Rows into Columns |
| vecmat | Multiply a Matrix by a Vector |
| vennCounts | Venn Diagrams |
| vennDiagram | Venn Diagrams |
| volcanoplot | Volcano Plot |
| write.fit | Write MArrayLM Object to a File |
| wtarea | Spot Quality Weights |
| wtflags | Spot Quality Weights |
| wtIgnore.Filter | Spot Quality Weights |
| zscoreGamma | z-score equivalents |
| zscoreT | z-score equivalents |
| [.MAList | Subset RGList, MAList or MArrayLM Objects |
| [.MArrayLM | Subset RGList, MAList or MArrayLM Objects |
| [.RGList | Subset RGList, MAList or MArrayLM Objects |