| 01Introduction | Introduction to the LIMMA Package |
| 02classes | Topic: Classes Defined by this Package |
| 03reading | Topic: Reading Microarray Data from Files |
| 04Background | Topic: Background Correction |
| 05Normalization | Topic: Normalization of Microarray Data |
| 06linearmodels | Topic: Linear Models for Microarrays |
| 07SingleChannel | Topic: Individual Channel Analysis of Two-Color Microarrays |
| 08Tests | Topic: Hypothesis Testing for Linear Models |
| 09Diagnostics | Topic: Diagnostics and Quality Assessment |
| 10GeneSetTests | Topic: Gene Set Tests |
| 11RNAseq | Topic: Analysis of RNA-seq Data |
| alias2Symbol | Convert Gene Aliases to Official Gene Symbols |
| anova-method | ANOVA Table - method |
| arrayWeights | Array Quality Weights |
| arrayWeightsQuick | Array Quality Weights |
| asdataframe | Turn a Microarray Linear Model Object into a Dataframe |
| asmalist | Convert marrayNorm Object to an MAList Object |
| asmatrix | Turn a Microarray Data Object into a Matrix |
| asMatrixWeights | asMatrixWeights |
| auROC | Area Under Receiver Operating Curve |
| avearrays | Average Over Replicate Arrays |
| avedups | Average Over Duplicate Spots |
| avereps | Average Over Irregular Replicate Probes |
| backgroundcorrect | 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... |
| cbind | Combine RGList, MAList, EList or EListRaw Objects |
| changelog | Change Log |
| channel2M | Convert Individual Channel Design Matrix to M-A Format |
| chooseLowessSpan | Choose Span for Local-Weighted Regression Smoothing |
| classifytestsF | Genewise Nested F-Tests |
| 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 |
| coolmap | Heatmap of gene expression values |
| cumOverlap | Cumulative Overlap Analysis of Ordered Lists |
| decideTests | Multiple Testing Across Genes and Contrasts |
| detectionPValue | Detection P-Values from Negative Controls |
| diffSplice | Test for Differential Splicing |
| dim | Retrieve the Dimensions of an RGList, MAList or MArrayLM... |
| dimnames | Retrieve the Dimension Names of an RGList, MAList, EList,... |
| dupcor | Correlation Between Duplicates |
| ebayes | Empirical Bayes Statistics for Differential Expression |
| EList | Expression List (EList) class |
| exprsMA | Extract Log-Expression Matrix from MAList |
| fitfdist | Moment Estimation of Scaled F-Distribution |
| fitGammaIntercept | Fit Intercept to Vector of Gamma Distributed Variates |
| fitmixture | Fit Mixture Model by Non-Linear Least Squares |
| fitted.MArrayLM | Fitted Values Method for MArrayLM Fits |
| genas | Genuine Association of Gene Expression Profiles |
| geneSetTest | Mean-rank Gene Set Test |
| getEAWP | Extract Basic Data from Expression Data Objects |
| getlayout | 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... |
| goana | Gene Ontology or KEGG Pathway Analysis |
| gridspotrc | Row and Column Positions on Microarray |
| head | Return the First to Last Part of a Data Object |
| 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 |
| intraspotCorrelation | Intra-Spot Correlation for Two Color Data |
| isfullrank | Check for Full Column Rank |
| isnumeric | Test for Numeric Argument |
| kooperberg | Kooperberg Model-Based Background Correction for GenePix data |
| LargeDataObject | Large Data Object - class |
| limmaUsersGuide | View Limma User's Guide |
| lmFit | Linear Model for Series of Arrays |
| lmscFit | Fit Linear Model to Individual Channels of Two-Color Data |
| lm.series | Fit Linear Model to Microrray Data by Ordinary Least Squares |
| loessfit | Univariate Lowess With Prior Weights |
| logcosh | Logarithm of cosh |
| logsumexp | Log Sum of Exponentials |
| ma3x3 | Two dimensional Moving Averages with 3x3 Window |
| makeContrasts | Construct Matrix of Custom Contrasts |
| makeunique | Make Values of Character Vector Unique |
| malist | M-value, A-value Expression List - class |
| marraylm | Microarray Linear Model Fit - class |
| mdplot | Mean-Difference Plot |
| merge | Merge RGList or MAList Data Objects |
| 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 |
| nec | NormExp Background Correction and Normalization Using Control... |
| normalizebetweenarrays | Normalize Between Arrays |
| normalizeCyclicLoess | Normalize Columns of a Matrix by Cyclic Loess |
| normalizeMedianAbsValues | Normalize Columns of a Matrix to have the Median Absolute... |
| normalizeprintorder | Print-Order Normalization |
| normalizequantiles | Normalize Columns of a Matrix to have the same Quantiles |
| normalizeRobustSpline | Normalize Single Microarray Using Shrunk Robust Splines |
| normalizeVSN | Variance Stabilizing Normalization (vsn) |
| normalizeWithinArrays | Normalize Within Arrays |
| normexpfit | Fit Normal+Exp Convolution Model to Observed Intensities |
| normexpfitcontrol | Normexp Model Parameter Estimation Aided by Negative Controls |
| normexpfitdetectionp | Estimate Normexp Model Parameter Using Negative Controls... |
| normexpsignal | Expected Signal Given Observed Foreground Under Normal+Exp... |
| plotDensities | Plot Expression Densities |
| plotExonJunc | Differential splicing plot with junctions |
| plotExons | Plot exons of differentially expressed gene |
| plotFB | FB-Plot |
| plotlines | plotlines |
| plotma | MA-Plot of Expression Data |
| plotma3by2 | Write MA-Plots to Files |
| plotMD | Mean-Difference Plot of Expression Data |
| plotMDS | Multidimensional scaling plot of distances between gene... |
| plotprinttiploess | MA Plots by Print-Tip Group |
| plotRLDF | Plot of regularized linear discriminant functions for... |
| 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 | Print Layout - class |
| printorder | Identify Order in which Spots were Printed |
| printtipWeights | Sub-array Quality Weights |
| propexpr | Estimate Proportion of Expressed Probes |
| propTrueNull | Estimate Proportion of True Null Hypotheses |
| protectMetachar | Protect Metacharacters |
| qqt | Student's t or Fisher's F Quantile-Quantile Plot |
| qualwt | Spot Quality Weights for Spotted Microarrays |
| rankSumTestwithCorrelation | Two Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For... |
| read.columns | Read specified columns from a file |
| readgal | Read a GAL file |
| readGPRHeader | Read Header Information from Microarray Raw Data 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 |
| readImaGeneHeader | Read ImaGene Header Information |
| read.maimages | Read RGList or EListRaw from Image Analysis Output Files |
| 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 |
| rglist | Red, Green Intensity List - class |
| roast | Rotation Gene Set Tests |
| romer | Rotation Gene Set Enrichment Analysis |
| selectmodel | Select Appropriate Linear Model |
| squeezeVar | Squeeze Sample Variances |
| strsplit2 | Split Composite Names |
| subsetting | Subset RGList, MAList, EListRaw, EList, MArrayLM or... |
| summary | Summaries of Microarray Data Objects |
| targetsA2C | Convert Two-Color Targets Dataframe from One-Row-Per-Array to... |
| TestResults | Matrix of Test Results - class |
| tmixture | Estimate Scale Factor in Mixture of t-Distributions |
| topGO | 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 |
| tricubeMovingAverage | Moving Average Smoother With Tricube Weights |
| trigammainverse | Inverse Trigamma Function |
| trimWhiteSpace | Trim Leading and Trailing White Space |
| uniquegenelist | Eliminate Duplicate Names from the Gene List |
| unwrapdups | Unwrap Duplicate Spot Values from Rows into Columns |
| venn | Venn Diagrams |
| volcanoplot | Volcano Plot |
| voom | Transform RNA-Seq Data Ready for Linear Modelling |
| vooma | Convert Mean-Variance Trend to Observation-specific Precision... |
| voomWithQualityWeights | Combining observational-level with sample-specific quality... |
| weightedLowess | LOWESS Smoother with Prior Weights |
| weightedmedian | Weighted Median |
| writefit | Write MArrayLM Object to a File |
| wsva | Weighted Surrogate Variable Analysis |
| zscore | Transform non-normal random deviates to standard normal |
| zscoreT | Transform t-statistics to standard normal |
