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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
| 01.Introduction | Introduction to the LIMMA Package |
| 02.Classes | Classes Defined by this Package |
| 03.ReadingData | Reading Microarray Data from Files |
| 04.Background | Background Correction |
| 05.Normalization | Normalization of Microarray Data |
| 06.LinearModels | Linear Models for Microarrays |
| 07.SingleChannel | Individual Channel Analysis of Two-Color Microarrays |
| 08.Tests | Hypothesis Testing for Linear Models |
| 09.Diagnostics | Diagnostics and Quality Assessment |
| 10.Other | Other Functions |
| alias2Symbol | Convert Gene Alias to Official Gene Symbols |
| 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 |
| arrayWeightsSimple | 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.EList | Turn a Microarray Data Object into a Matrix |
| as.matrix.EListRaw | Turn a Microarray Data Object into a Matrix |
| as.matrix.ExpressionSet | Turn a Microarray Data Object into a Matrix |
| as.matrix.LumiBatch | 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.PLMset | Turn a Microarray Data Object into a Matrix |
| as.matrix.RGList | Turn a Microarray Data Object into a Matrix |
| as.matrix.vsn | Turn a Microarray Data Object into a Matrix |
| asMatrixWeights | asMatrixWeights |
| auROC | Area Under Receiver Operating Curve |
| avedups | Average Over Duplicate Spots |
| avedups.default | Average Over Duplicate Spots |
| avedups.MAList | Average Over Duplicate Spots |
| avereps | Average Over Irregular Replicate Spots |
| avereps.default | Average Over Irregular Replicate Spots |
| avereps.MAList | Average Over Irregular Replicate Spots |
| backgroundCorrect | Correct Intensities for Background |
| barcodeplot | Gene Set Test |
| blockDiag | Block Diagonal Matrix |
| bwss | Between and within sums of squares |
| bwss.matrix | Between and within sums of squares for matrix |
| cbind.EList | Combine RGList, MAList, EList or EListRaw Objects |
| cbind.EListRaw | Combine RGList, MAList, EList or EListRaw Objects |
| cbind.MAList | Combine RGList, MAList, EList or EListRaw Objects |
| cbind.RGList | Combine RGList, MAList, EList or EListRaw Objects |
| changeLog | Limma Change Log |
| classifyTestsF | Multiple Testing Genewise Across Contrasts |
| classifyTestsP | Multiple Testing Genewise Across Contrasts |
| classifyTestsT | Multiple Testing Genewise Across Contrasts |
| 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 | Multiple Testing Across Genes and Contrasts |
| designI2A | Convert Individual Channel Design Matrix to M-A Format |
| designI2M | Convert Individual Channel Design Matrix to M-A Format |
| dim.EList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
| dim.EListRaw | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
| 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.EList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
| dimnames.EListRaw | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
| dimnames.MAList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
| dimnames.MArrayLM | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
| dimnames.RGList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
| dimnames<-.EList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
| dimnames<-.EListRaw | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
| dimnames<-.MAList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
| dimnames<-.RGList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object |
| duplicateCorrelation | Correlation Between Duplicates |
| eBayes | Empirical Bayes Statistics for Differential Expression |
| ebayes | Empirical Bayes Statistics for Differential Expression |
| EList-class | Expression List - class |
| EListRaw-class | Expression List - class |
| exprs.MA | Extract Log-Expression Matrix from MAList |
| fitFDist | Moment Estimation of Scaled F-Distribution |
| fitted.MArrayLM | Fitted Values Method for MArrayLM Fits |
| FStat | Multiple Testing Genewise Across Contrasts |
| geneSetTest | Gene Set Test |
| getDupSpacing | Extract the Print Layout of an Array from the GAL File |
| getEAWP | Extract Basic Data from Microarray Data Objects |
| 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 | Fit Linear Model to Microarray Data by Generalized Least Squares |
| gridc | Row and Column Positions on Microarray |
| gridr | Row and Column Positions on Microarray |
| 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.EList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
| length.EListRaw | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object |
| 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 |
| limma | Introduction to the LIMMA Package |
| limmaUsersGuide | View Limma User's Guide |
| lm.series | Fit Linear Model to Microrray Data by Ordinary Least Squares |
| lmFit | Linear Model for Series of Arrays |
| lmscFit | Fit Linear Model to Individual Channels of Two-Color Data |
| loessFit | Fast Simple Loess |
| 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 |
| mdplot | mdplot |
| merge.MAList | Merge RGList or MAList Data Objects |
| merge.RGList | Merge RGList or MAList Data Objects |
| mergeScans | Merge two scans of two-color arrays |
| mergeScansRG | Merge two scans of two-color arrays |
| modelMatrix | Construct Design Matrix |
| modifyWeights | modifyWeights |
| mrlm | Fit Linear Model to Microrray Data by Robust Regression |
| nonEstimable | Check for Full Column Rank |
| normalizeBetweenArrays | Normalize Between Arrays |
| normalizeForPrintorder | Print-Order Normalization |
| normalizeForPrintorder.rg | Print-Order Normalization |
| normalizeMedianAbsValues | Normalize Columns of a Matrix to have the Median Absolute Value |
| normalizeQuantiles | Normalize Columns of a Matrix to have the same Quantiles |
| normalizeRobustSpline | Normalize Single Microarray Using Shrunk Robust Splines |
| normalizeWithinArrays | Normalize Within Arrays |
| normexp.fit | Fit Normal+Exp Convolution Model to Observed Intensities |
| normexp.signal | Expected Signal Given Observed Foreground Under Normal+Exp Model |
| plotDensities | Individual-channel Densities Plot |
| plotFB | FB-Plot |
| plotlines | plotlines |
| plotMA | MA-Plot |
| plotMA3by2 | Write MA-Plots to Files |
| plotMDS | Multidimensional scaling plot of microarray data |
| plotPrintorder | Print-Order Normalization |
| plotPrintTipLoess | MA Plots by Print-Tip Group |
| plotSA | Sigma vs A plot for microarray linear model |
| 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 |
| printtipWeights | Sub-array Quality Weights |
| printtipWeightsSimple | Sub-array Quality Weights |
| protectMetachar | Protect Metacharacters |
| qqt | Student's t Quantile-Quantile Plot |
| QualityWeights | Spot Quality Weights |
| rbind.EList | Combine RGList, MAList, EList or EListRaw Objects |
| rbind.EListRaw | Combine RGList, MAList, EList or EListRaw Objects |
| rbind.MAList | Combine RGList, MAList, EList or EListRaw Objects |
| rbind.RGList | Combine RGList, MAList, EList or EListRaw Objects |
| read.columns | Read specified columns from a file |
| read.imagene | Read RGList or EListRaw from Image Analysis Output Files |
| read.maimages | Read RGList or EListRaw from Image Analysis Output Files |
| readGAL | Read a GAL file |
| readGenericHeader | Read Header Information from Image Analysis Raw Data 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 |
| removeBatchEffect | Remove Batch Effect |
| removeExt | Remove Common Extension from File Names |
| residuals.MArrayLM | Extract Residuals from MArrayLM Fit |
| RG.MA | Normalize Within Arrays |
| RGList-class | Red, Green Intensity List - class |
| roast | Rotation Gene Set Tests |
| romer | Rotation Gene Set Enrichment Analysis |
| selectModel | Select Appropriate Linear Model |
| show,LargeDataObject-method | Large Data Object - class |
| show,TestResults-method | Matrix of Test Results - class |
| spotc | Row and Column Positions on Microarray |
| spotr | Row and Column Positions on Microarray |
| squeezeVar | Smooth Sample Variances |
| strsplit2 | Split Composite Names |
| summary.EList | Summaries of Microarray Data Objects |
| summary.EListRaw | Summaries of Microarray Data Objects |
| 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 |
| symbols2indices | Make Gene Set Indices from Symbols |
| 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 |
| topTableF | Table of Top Genes from Linear Model Fit |
| topTreat | Table of Top Genes from Linear Model Fit |
| treat | Empirical Bayes Statistics for Differential Expression |
| 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 |
| vennCounts | Venn Diagrams |
| vennDiagram | Venn Diagrams |
| volcanoplot | Volcano Plot |
| weighted.median | Weighted Median |
| 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 |
| [.EList | Subset RGList, MAList, EList or MArrayLM Objects |
| [.EListRaw | Subset RGList, MAList, EList or MArrayLM Objects |
| [.MAList | Subset RGList, MAList, EList or MArrayLM Objects |
| [.MArrayLM | Subset RGList, MAList, EList or MArrayLM Objects |
| [.RGList | Subset RGList, MAList, EList or MArrayLM Objects |