A B C D E F G H I K L M N P Q R S T U V W Z misc
| limma-package | Introduction to the LIMMA Package |
| alias2Symbol | Convert Gene Aliases to Official Gene Symbols |
| alias2SymbolTable | Convert Gene Aliases 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.EList | Turn a Microarray Linear Model Object into a Dataframe |
| as.data.frame.EListRaw | Turn a Microarray Linear Model Object into a Dataframe |
| as.data.frame.MAList | Turn a Microarray Linear Model Object into a Dataframe |
| 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 |
| avearrays | Average Over Replicate Arrays |
| avearrays.default | Average Over Replicate Arrays |
| avearrays.EList | Average Over Replicate Arrays |
| avearrays.MAList | Average Over Replicate Arrays |
| avedups | Average Over Duplicate Spots |
| avedups.default | Average Over Duplicate Spots |
| avedups.EList | Average Over Duplicate Spots |
| avedups.MAList | Average Over Duplicate Spots |
| avereps | Average Over Irregular Replicate Probes |
| avereps.default | Average Over Irregular Replicate Probes |
| avereps.EList | Average Over Irregular Replicate Probes |
| avereps.EListRaw | Average Over Irregular Replicate Probes |
| avereps.MAList | Average Over Irregular Replicate Probes |
| avereps.RGList | Average Over Irregular Replicate Probes |
| backgroundCorrect | Correct Intensities for Background |
| backgroundCorrect.matrix | Correct Intensities for Background |
| barcodeplot | Barcode Enrichment Plot |
| beadCountWeights | Bead Count Weights for Illumina BeadChips |
| blockDiag | Block Diagonal Matrix |
| bwss | Between and within sums of squares |
| bwss.matrix | Between and within sums of squares for matrix |
| camera | Competitive Gene Set Test Accounting for Inter-gene Correlation |
| camera.default | Competitive Gene Set Test Accounting for Inter-gene Correlation |
| cbind | Combine RGList, MAList, EList or EListRaw Objects |
| 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-method | Red, Green Intensity List - class |
| contrastAsCoef | Reform a Design Matrix to that Contrasts Become Coefficients |
| 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 |
| diffSplice | Test for Differential Splicing |
| 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 |
| estimate.m0 | Estimate Proportion of True Null Hypotheses |
| exprs.MA | Extract Log-Expression Matrix from MAList |
| fitFDist | Moment Estimation of Scaled F-Distribution |
| fitFDistRobustly | Moment Estimation of Scaled F-Distribution |
| fitGammaIntercept | Fit Intercept to Vector of Gamma Distributed Variates |
| fitted.MArrayLM | Fitted Values Method for MArrayLM Fits |
| fry | Rotation Gene Set Tests |
| fry.default | Rotation Gene Set Tests |
| FStat | Multiple Testing Genewise Across Contrasts |
| genas | Genuine Association of Gene Expression Profiles |
| geneSetTest | Mean-rank Gene Set Test |
| getDupSpacing | Extract the Print Layout of an Array from the GAL File |
| getEAWP | Extract Basic Data from Expression Data Objects |
| getGeneKEGGLinks | Gene Ontology or KEGG Pathway Analysis |
| getKEGGPathwayNames | Gene Ontology or KEGG Pathway Analysis |
| 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 |
| goana | Gene Ontology or KEGG Pathway Analysis |
| goana.default | Gene Ontology or KEGG Pathway Analysis |
| goana.MArrayLM | Gene Ontology or KEGG Pathway Analysis |
| 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 |
| ids2indices | Convert Gene Identifiers to Indices for Gene Sets |
| imageplot | Image Plot of Microarray Statistics |
| imageplot3by2 | Write Imageplots to Files |
| interGeneCorrelation | Competitive Gene Set Test Accounting for Inter-gene Correlation |
| intraspotCorrelation | Intra-Spot Correlation for Two Color Data |
| is.fullrank | Check for Full Column Rank |
| isNumeric | Test for Numeric Argument |
| kegga | Gene Ontology or KEGG Pathway Analysis |
| kegga.default | Gene Ontology or KEGG Pathway Analysis |
| kegga.MArrayLM | Gene Ontology or KEGG Pathway Analysis |
| kooperberg | Kooperberg Model-Based Background Correction for GenePix data |
| 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 | Univariate Lowess With Prior Weights |
| 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 | Mean-Difference Plot |
| MDS-class | Multidimensional scaling plot of distances between gene expression profiles |
| merge.EList | Merge RGList or MAList Data Objects |
| merge.EListRaw | Merge RGList or MAList Data Objects |
| 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 | Modify Matrix of Weights By Control Status of Rows |
| mrlm | Fit Linear Model to Microrray Data by Robust Regression |
| mroast | Rotation Gene Set Tests |
| mroast.default | Rotation Gene Set Tests |
| nec | NormExp Background Correction and Normalization Using Control Probes |
| neqc | NormExp Background Correction and Normalization Using Control Probes |
| nonEstimable | Check for Full Column Rank |
| normalizeBetweenArrays | Normalize Between Arrays |
| normalizeCyclicLoess | Normalize Columns of a Matrix by Cyclic Loess |
| normalizeForPrintorder | Print-Order Normalization |
| normalizeForPrintorder.rg | Print-Order Normalization |
| normalizeMedianAbsValues | Normalize Columns of a Matrix to have the Median Absolute Value |
| normalizeMedianValues | 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 |
| normalizeVSN | Variance Stabilizing Normalization (vsn) |
| normalizeVSN.default | Variance Stabilizing Normalization (vsn) |
| normalizeVSN.EListRaw | Variance Stabilizing Normalization (vsn) |
| normalizeVSN.RGList | Variance Stabilizing Normalization (vsn) |
| normalizeWithinArrays | Normalize Within Arrays |
| normexp.fit | Fit Normal+Exp Convolution Model to Observed Intensities |
| normexp.fit.control | Normexp Model Parameter Estimation Aided by Negative Controls |
| normexp.fit.detection.p | Estimate Normexp Model Parameter Using Negative Controls Inferred from Regular Probes |
| normexp.signal | Expected Signal Given Observed Foreground Under Normal+Exp Model |
| plotDensities | Plot Expression Densities |
| plotDensities.default | Plot Expression Densities |
| plotDensities.EList | Plot Expression Densities |
| plotDensities.EListRaw | Plot Expression Densities |
| plotDensities.MAList | Plot Expression Densities |
| plotDensities.RGList | Plot Expression Densities |
| plotExons | Plot exons of differentially expressed gene |
| plotFB | FB-Plot |
| plotFB.default | FB-Plot |
| plotFB.EListRaw | FB-Plot |
| plotFB.RGList | FB-Plot |
| plotlines | plotlines |
| plotMA | MA-Plot of Expression Data |
| plotMA.default | MA-Plot of Expression Data |
| plotMA.EList | MA-Plot of Expression Data |
| plotMA.EListRaw | MA-Plot of Expression Data |
| plotMA.MAList | MA-Plot of Expression Data |
| plotMA.MArrayLM | MA-Plot of Expression Data |
| plotMA.RGList | MA-Plot of Expression Data |
| plotMA3by2 | Write MA-Plots to Files |
| plotMD | Mean-Difference Plot of Expression Data |
| plotMD.default | Mean-Difference Plot of Expression Data |
| plotMD.EList | Mean-Difference Plot of Expression Data |
| plotMD.EListRaw | Mean-Difference Plot of Expression Data |
| plotMD.MAList | Mean-Difference Plot of Expression Data |
| plotMD.MArrayLM | Mean-Difference Plot of Expression Data |
| plotMD.RGList | Mean-Difference Plot of Expression Data |
| plotMDS | Multidimensional scaling plot of distances between gene expression profiles |
| plotMDS.default | Multidimensional scaling plot of distances between gene expression profiles |
| plotMDS.MDS | Multidimensional scaling plot of distances between gene expression profiles |
| plotPrintorder | Print-Order Normalization |
| plotPrintTipLoess | MA Plots by Print-Tip Group |
| plotRLDF | Plot of regularized linear discriminant functions for microarray data |
| plotSA | Sigma vs A plot for microarray linear model |
| plotSplice | Differential splicing plot |
| plotWithHighlights | Scatterplot With Highlighting of Special Points |
| poolVar | Pool Sample Variances with Unequal Variances |
| predFCm | Predictive log fold change for microarrays |
| 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 |
| propexpr | Estimate Proportion of Expressed Probes |
| propTrueNull | Estimate Proportion of True Null Hypotheses |
| protectMetachar | Protect Metacharacters |
| qqf | Student's t Quantile-Quantile Plot |
| qqt | Student's t Quantile-Quantile Plot |
| QualityWeights | Spot Quality Weights |
| rankSumTestWithCorrelation | Two Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For Correlation |
| 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.idat | Read Illumina expression data directly from IDAT files |
| read.ilmn | Read Illumina Expression Data |
| read.ilmn.targets | Read Illumina Data from a Target Dataframe |
| 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 Microarray Raw Data File |
| readGPRHeader | Read Header Information from Microarray Raw Data File |
| readImaGeneHeader | Read ImaGene Header Information |
| readSMDHeader | Read Header Information from Microarray 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 |
| Roast-class | Rotation Gene Set Tests |
| roast.default | Rotation Gene Set Tests |
| romer | Rotation Gene Set Enrichment Analysis |
| romer.default | Rotation Gene Set Enrichment Analysis |
| selectModel | Select Appropriate Linear Model |
| show-method | Large Data Object - class |
| show-method | Matrix of Test Results - class |
| show-method | Multidimensional scaling plot of distances between gene expression profiles |
| show-method | Rotation Gene Set Tests |
| spotc | Row and Column Positions on Microarray |
| spotr | Row and Column Positions on Microarray |
| squeezeVar | Squeeze Sample Variances |
| strsplit2 | Split Composite Names |
| subsetListOfArrays | Subset RGList, MAList, EListRaw, EList or MArrayLM Objects |
| subsetting | Subset RGList, MAList, EListRaw, EList or MArrayLM Objects |
| 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 |
| 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 |
| topGO | Table of Top GO Terms or Top KEGG Pathways |
| topKEGG | Table of Top GO Terms or Top KEGG Pathways |
| topRomer | Top Gene Set Testing Results from Romer |
| topSplice | Top table of differentially spliced genes or exons |
| 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 |
| tricubeMovingAverage | Moving Average Smoother With Tricube Weights |
| 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 |
| voom | Transform RNA-Seq Data Ready for Linear Modelling |
| vooma | Convert Mean-Variance Trend to Observation-specific Precision Weights for Microarray Data |
| voomaByGroup | Convert Mean-Variance Trend to Observation-specific Precision Weights for Microarray Data |
| voomWithQualityWeights | Combining observational-level with sample-specific quality weights for RNA-seq analysis |
| weighted.median | Weighted Median |
| weightedLowess | Lowess fit with weighting |
| wilcoxGST | Mean-rank Gene Set Test |
| write.fit | Write MArrayLM Object to a File |
| wtarea | Spot Quality Weights |
| wtflags | Spot Quality Weights |
| wtIgnore.Filter | Spot Quality Weights |
| zscore | Z-score Equivalents |
| zscoreGamma | Z-score Equivalents |
| zscoreHyper | Z-score Equivalents |
| zscoreT | Z-score Equivalents |
| 01.Introduction | Introduction to the LIMMA Package |
| 02.Classes | Topic: Classes Defined by this Package |
| 03.ReadingData | Topic: Reading Microarray Data from Files |
| 04.Background | Topic: Background Correction |
| 05.Normalization | Topic: Normalization of Microarray Data |
| 06.LinearModels | Topic: Linear Models for Microarrays |
| 07.SingleChannel | Topic: Individual Channel Analysis of Two-Color Microarrays |
| 08.Tests | Topic: Hypothesis Testing for Linear Models |
| 09.Diagnostics | Topic: Diagnostics and Quality Assessment |
| 10.GeneSetTests | Topic: Gene Set Tests |
| 11.RNAseq | Topic: Analysis of RNA-seq Data |
| [.EList | Subset RGList, MAList, EListRaw, EList or MArrayLM Objects |
| [.EListRaw | Subset RGList, MAList, EListRaw, EList or MArrayLM Objects |
| [.MAList | Subset RGList, MAList, EListRaw, EList or MArrayLM Objects |
| [.MArrayLM | Subset RGList, MAList, EListRaw, EList or MArrayLM Objects |
| [.RGList | Subset RGList, MAList, EListRaw, EList or MArrayLM Objects |