| Introduction to the LIMMA Package | limma-package 01.Introduction limma |
| Topic: Classes Defined by this Package | 02.Classes |
| Topic: Reading Microarray Data from Files | 03.ReadingData |
| Topic: Background Correction | 04.Background |
| Topic: Normalization of Microarray Data | 05.Normalization |
| Topic: Linear Models for Microarrays | 06.LinearModels |
| Topic: Individual Channel Analysis of Two-Color Microarrays | 07.SingleChannel |
| Topic: Hypothesis Testing for Linear Models | 08.Tests |
| Topic: Diagnostics and Quality Assessment | 09.Diagnostics |
| Topic: Gene Set Tests | 10.GeneSetTests |
| Topic: Analysis of RNA-seq Data | 11.RNAseq |
| Convert Gene Aliases to Official Gene Symbols | alias2Symbol alias2SymbolTable alias2SymbolUsingNCBI |
| ANOVA Table - method | anova.MAList |
| Array Quality Weights | arrayWeights |
| Array Quality Weights | arrayWeightsQuick |
| Turn a Microarray Linear Model Object into a Dataframe | as.data.frame.EList as.data.frame.EListRaw as.data.frame.MAList as.data.frame.MArrayLM |
| Convert marrayNorm Object to an MAList Object | as.MAList |
| Turn a Microarray Data Object into a Matrix | as.matrix.EList as.matrix.EListRaw as.matrix.ExpressionSet as.matrix.LumiBatch as.matrix.MAList as.matrix.MArrayLM as.matrix.marrayNorm as.matrix.PLMset as.matrix.RGList as.matrix.vsn |
| asMatrixWeights | asMatrixWeights |
| Area Under Receiver Operating Curve | auROC |
| Average Over Replicate Arrays | avearrays avearrays.default avearrays.EList avearrays.MAList |
| Average Over Duplicate Spots | avedups avedups.default avedups.EList avedups.MAList |
| Average Over Irregular Replicate Probes | avereps avereps.default avereps.EList avereps.EListRaw avereps.MAList avereps.RGList |
| Correct Intensities for Background | backgroundCorrect backgroundCorrect.matrix |
| Barcode Enrichment Plot | barcodeplot |
| Bead Count Weights for Illumina BeadChips | beadCountWeights |
| Block Diagonal Matrix | blockDiag |
| Between and within sums of squares | bwss |
| Between and within sums of squares for matrix | bwss.matrix |
| Competitive Gene Set Test Accounting for Inter-gene Correlation | camera camera.default cameraPR cameraPR.default interGeneCorrelation |
| Combine RGList, MAList, EList or EListRaw Objects | cbind cbind.EList cbind.EListRaw cbind.MAList cbind.RGList rbind.EList rbind.EListRaw rbind.MAList rbind.RGList |
| Change Log | changeLog |
| Choose Span for Local-Weighted Regression Smoothing | chooseLowessSpan |
| Genewise Nested F-Tests | classifyTestsF |
| Reform a Design Matrix to that Contrasts Become Coefficients | contrastAsCoef |
| Compute Contrasts from Linear Model Fit | contrasts.fit |
| Set Status of each Spot from List of Spot Types | controlStatus |
| Heatmap of gene expression values | coolmap |
| Cumulative Overlap Analysis of Ordered Lists | cumOverlap |
| Multiple Testing Across Genes and Contrasts | decideTests decideTests.default decideTests.MArrayLM |
| Convert Individual Channel Design Matrix to M-A Format | designI2A designI2M |
| Detection P-Values from Negative Controls | detectionPValues detectionPValues.default detectionPValues.EListRaw |
| Test for Differential Splicing | diffSplice |
| Retrieve the Dimensions of an RGList, MAList or MArrayLM Object | dim.EList dim.EListRaw dim.MAList dim.MArrayLM dim.RGList |
| Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object | dimnames.EList dimnames.EListRaw dimnames.MAList dimnames.MArrayLM dimnames.RGList dimnames<-.EList dimnames<-.EListRaw dimnames<-.MAList dimnames<-.RGList |
| Correlation Between Duplicates or Within Blocks | duplicateCorrelation |
| Empirical Bayes Statistics for Differential Expression | eBayes treat |
| Expression List (EList) class | EList-class EListRaw-class |
| Extract Log-Expression Matrix from MAList | exprs.MA |
| Moment Estimation of Scaled F-Distribution | fitFDist fitFDistRobustly |
| Fit Intercept to Vector of Gamma Distributed Variates | fitGammaIntercept |
| Fit Mixture Model by Non-Linear Least Squares | fitmixture |
| Fitted Values Method for MArrayLM Fits | fitted.MArrayLM |
| Genuine Association of Gene Expression Profiles | genas |
| Mean-rank Gene Set Test | geneSetTest wilcoxGST |
| Extract Basic Data from Expression Data Objects | getEAWP |
| Extract the Print Layout of an Array from the GAL File | getDupSpacing getLayout getLayout2 |
| Get Numerical Spacing | getSpacing |
| Fit Linear Model to Microarray Data by Generalized Least Squares | gls.series |
| Gene Ontology or KEGG Pathway Analysis | getGeneKEGGLinks getKEGGPathwayNames goana goana.default goana.MArrayLM kegga kegga.default kegga.MArrayLM |
| Estimate DE Trend for Gene Ontology or KEGG Pathway Analysis | goanaTrend |
| Row and Column Positions on Microarray | gridc gridr spotc spotr |
| Return the First to Last Part of a Data Object | head.EList head.EListRaw head.MAList head.MArrayLM head.RGList head.TestResults tail.EList tail.EListRaw tail.MAList tail.MArrayLM tail.RGList tail.TestResults |
| Stemmed Heat Diagram | heatDiagram heatdiagram |
| Prompt for Method Help Topics | helpMethods |
| Convert Gene Identifiers to Indices for Gene Sets | ids2indices |
| Image Plot of Microarray Statistics | imageplot |
| Write Imageplots to Files | imageplot3by2 |
| Intra-Spot Correlation for Two Color Data | intraspotCorrelation |
| Check for Full Column Rank | is.fullrank nonEstimable |
| Test for Numeric Argument | isNumeric |
| Kooperberg Model-Based Background Correction for GenePix data | kooperberg |
| Large Data Object - class | LargeDataObject-class show,LargeDataObject-method |
| View Limma User's Guide | limmaUsersGuide |
| Fit Linear Model to Microrray Data by Ordinary Least Squares | lm.series |
| Linear Model for Series of Arrays | lmFit |
| Fit Linear Model to Individual Channels of Two-Color Data | lmscFit |
| Univariate Lowess With Prior Weights | loessFit |
| Logarithm of cosh | logcosh |
| Log Sum of Exponentials | logsumexp |
| Two dimensional Moving Averages with 3x3 Window | ma3x3.matrix ma3x3.spottedarray |
| Construct Matrix of Custom Contrasts | makeContrasts |
| Make Values of Character Vector Unique | makeUnique |
| M-value, A-value Expression List - class | MAList-class |
| Microarray Linear Model Fit - class | MArrayLM-class |
| Mean-Difference Plot | mdplot |
| Merge RGList or MAList Data Objects | merge.EList merge.EListRaw merge.MAList merge.RGList |
| Merge two scans of two-color arrays | mergeScans mergeScansRG |
| Construct Design Matrix | modelMatrix uniqueTargets |
| Modify Matrix of Weights By Control Status of Rows | modifyWeights |
| Fit Linear Model to Microrray Data by Robust Regression | mrlm |
| NormExp Background Correction and Normalization Using Control Probes | nec neqc |
| Normalize Between Arrays | normalizeBetweenArrays |
| Normalize Columns of a Matrix by Cyclic Loess | normalizeCyclicLoess |
| Print-Order Normalization | normalizeForPrintorder normalizeForPrintorder.rg plotPrintorder |
| Normalize Columns of a Matrix to have the Median Absolute Value | normalizeMedianAbsValues normalizeMedianValues |
| Normalize Columns of a Matrix to have the same Quantiles | normalizeQuantiles |
| Normalize Single Microarray Using Shrunk Robust Splines | normalizeRobustSpline |
| Variance Stabilizing Normalization (vsn) | normalizeVSN normalizeVSN.default normalizeVSN.EListRaw normalizeVSN.RGList |
| Normalize Within Arrays | MA.RG normalizeWithinArrays RG.MA |
| Fit Normal+Exp Convolution Model to Observed Intensities | normexp.fit |
| Normexp Model Parameter Estimation Aided by Negative Controls | normexp.fit.control |
| Estimate Normexp Model Parameter Using Negative Controls Inferred from Regular Probes | normexp.fit.detection.p |
| Expected Signal Given Observed Foreground Under Normal+Exp Model | normexp.signal |
| Plot Expression Densities | plotDensities plotDensities.default plotDensities.EList plotDensities.EListRaw plotDensities.MAList plotDensities.RGList |
| Differential splicing plot with junctions | plotExonJunc |
| Plot exons of differentially expressed gene | plotExons |
| FB-Plot | plotFB plotFB.default plotFB.EListRaw plotFB.RGList |
| plotlines | plotlines |
| MA-Plot of Expression Data | plotMA plotMA.default plotMA.EList plotMA.EListRaw plotMA.MAList plotMA.MArrayLM plotMA.RGList |
| Write MA-Plots to Files | plotMA3by2 |
| Mean-Difference Plot of Expression Data | plotMD plotMD.default plotMD.EList plotMD.EListRaw plotMD.MAList plotMD.MArrayLM plotMD.RGList |
| Multidimensional scaling plot of distances between gene expression profiles | MDS-class plotMDS plotMDS.default plotMDS.MDS show,MDS-method |
| MA Plots by Print-Tip Group | plotPrintTipLoess |
| Plot of regularized linear discriminant functions for microarray data | plotRLDF |
| Sigma vs A plot for microarray linear model | plotSA |
| Differential splicing plot | plotSplice |
| Scatterplot With Highlighting of Special Points | plotWithHighlights |
| Pool Sample Variances with Unequal Variances | poolVar |
| Predictive log fold change for microarrays | predFCm |
| Print Leading Rows of Large Objects | printHead |
| Print Layout - class | PrintLayout-class |
| Identify Order in which Spots were Printed | printorder |
| Sub-array Quality Weights | printtipWeights printtipWeightsSimple |
| Estimate Proportion of Expressed Probes | propexpr |
| Estimate Proportion of True Null Hypotheses | convest estimate.m0 propTrueNull |
| Protect Metacharacters | protectMetachar |
| Student's t or Fisher's F Quantile-Quantile Plot | qqf qqt |
| Spot Quality Weights for Spotted Microarrays | QualityWeights wtarea wtflags wtIgnore.Filter |
| Two Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For Correlation | rankSumTestWithCorrelation |
| Read specified columns from a file | read.columns |
| Read Illumina expression data from IDAT files | read.idat |
| Read Illumina Expression Data | read.ilmn |
| Read Illumina Data from a Target Dataframe | read.ilmn.targets |
| Read RGList or EListRaw from Image Analysis Output Files | read.imagene read.maimages |
| Read a GAL file | readGAL |
| Read Header Information from Microarray Raw Data File | readGenericHeader readGPRHeader readSMDHeader |
| Read ImaGene Header Information | readImaGeneHeader |
| Read Spot Types File | readSpotTypes |
| Read Targets File | readTargets |
| Remove Batch Effect | removeBatchEffect |
| Remove Common Extension from File Names | removeExt |
| Extract Residuals from MArrayLM Fit | residuals.MArrayLM |
| Red, Green Intensity List - class | coerce,RGList,exprSet2-method RGList-class |
| Rotation Gene Set Tests | fry fry.default mroast mroast.default roast Roast-class roast.default show,Roast-method |
| Rotation Gene Set Enrichment Analysis | romer romer.default |
| Read Sample Characteristics From GEO Series Matrix File | sampleInfoFromGEO |
| Select Appropriate Linear Model | selectModel |
| Squeeze Sample Variances | squeezeVar |
| Split Composite Names | strsplit2 |
| Subset RGList, MAList, EListRaw, EList, MArrayLM or TestResults Objects | subsetListOfArrays subsetting [.EList [.EListRaw [.MAList [.MArrayLM [.RGList [.TestResults |
| Summaries of Microarray Data Objects | summary.EList summary.EListRaw summary.MAList summary.MArrayLM summary.RGList |
| Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel | array2channel targetsA2C |
| Matrix of Test Results - class | labels.TestResults levels.TestResults show,TestResults-method summary.TestResults TestResults-class unique.TestResults |
| Estimate Scale Factor in Mixture of t-Distributions | tmixture.matrix tmixture.vector |
| Table of Top GO Terms or Top KEGG Pathways | topGO topKEGG |
| Top Gene Set Testing Results from Romer | topRomer |
| Top table of differentially spliced genes or exons | topSplice |
| Table of Top Genes from Linear Model Fit | topTable topTableF topTreat |
| Moving Average Smoother With Tricube Weights | tricubeMovingAverage |
| Inverse Trigamma Function | trigammaInverse |
| Trim Leading and Trailing White Space | trimWhiteSpace |
| Eliminate Duplicate Names from the Gene List | uniquegenelist |
| Unwrap Duplicate Spot Values from Rows into Columns | unwrapdups |
| Venn Diagrams | vennCounts vennDiagram |
| Volcano Plot | volcanoplot |
| Transform RNA-Seq Counts for Linear Modeling With Precision Weights | voom |
| Convert Variance Trend to Observation Precision Weights for Microarray-style Data | vooma voomaByGroup |
| Apply vooma-lmFit Pipeline With Automatic Estimation of Sample Weights and Block Correlation | voomaLmFit |
| Transform RNA-Seq Counts for Linear Modeling With Precision and Sample Weights | voomWithQualityWeights |
| Weighted Median | weighted.median |
| LOWESS Smoother with Prior Weights | weightedLowess |
| Write MArrayLM Object to a File | write.fit |
| Weighted Surrogate Variable Analysis | wsva |
| Transform non-normal random deviates to standard normal | zscore zscoreGamma zscoreHyper |
| Transform t-statistics to standard normal | tZscore zscoreT |
