limma v3.28.14

by Gordon Smyth

Linear Models for Microarray Data

Data analysis, linear models and differential expression for microarray data.

Functions in limma

Name Description
03.ReadingData Topic: Reading Microarray Data from Files
anova.MAList-method ANOVA Table - method
arrayWeights Array Quality Weights
backgroundCorrect Correct Intensities for Background
avereps Average Over Irregular Replicate Probes
04.Background Topic: Background Correction
detectionPValues Detection P-Values from Negative Controls
dim Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
diffSplice Test for Differential Splicing
dimnames Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object
getSpacing Get Numerical Spacing
gls.series Fit Linear Model to Microarray Data by Generalized Least Squares
limmaUsersGuide View Limma User's Guide
lm.series Fit Linear Model to Microrray Data by Ordinary Least Squares
modifyWeights Modify Matrix of Weights By Control Status of Rows
mrlm Fit Linear Model to Microrray Data by Robust Regression
alias2Symbol Convert Gene Aliases to Official Gene Symbols
11.RNAseq Topic: Analysis of RNA-seq Data
bwss.matrix Between and within sums of squares for matrix
camera Competitive Gene Set Test Accounting for Inter-gene Correlation
controlStatus Set Status of each Spot from List of Spot Types
decideTests Multiple Testing Across Genes and Contrasts
getEAWP Extract Basic Data from Expression Data Objects
dupcor Correlation Between Duplicates
ebayes Empirical Bayes Statistics for Differential Expression
normalizeWithinArrays Normalize Within Arrays
plotMDS Multidimensional scaling plot of distances between gene expression profiles
normexp.fit Fit Normal+Exp Convolution Model to Observed Intensities
plotPrintTipLoess MA Plots by Print-Tip Group
printHead Print Leading Rows of Large Objects
PrintLayout Print Layout - class
09.Diagnostics Topic: Diagnostics and Quality Assessment
10.GeneSetTests Topic: Gene Set Tests
as.MAList Convert marrayNorm Object to an MAList Object
as.matrix Turn a Microarray Data Object into a Matrix
ma3x3 Two dimensional Moving Averages with 3x3 Window
read.ilmn Read Illumina Expression Data
read.ilmn.targets Read Illumina Data from a Target Dataframe
readSpotTypes Read Spot Types File
summary Summaries of Microarray Data Objects
readTargets Read Targets File
targetsA2C Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel
makeContrasts Construct Matrix of Custom Contrasts
mergeScans Merge two scans of two-color arrays
plotlines plotlines
modelMatrix Construct Design Matrix
plotMA MA-Plot of Expression Data
propexpr Estimate Proportion of Expressed Probes
is.fullrank Check for Full Column Rank
getLayout Extract the Print Layout of an Array from the GAL File
isNumeric Test for Numeric Argument
logcosh Logarithm of cosh
loessFit Univariate Lowess With Prior Weights
plotExons Plot exons of differentially expressed gene
unwrapdups Unwrap Duplicate Spot Values from Rows into Columns
venn Venn Diagrams
propTrueNull Estimate Proportion of True Null Hypotheses
read.maimages Read RGList or EListRaw from Image Analysis Output Files
readGAL Read a GAL file
roast Rotation Gene Set Tests
romer Rotation Gene Set Enrichment Analysis
TestResults-class Matrix of Test Results - class
plotWithHighlights Scatterplot With Highlighting of Special Points
plotSplice Differential splicing plot
tmixture Estimate Scale Factor in Mixture of t-Distributions
plotFB FB-Plot
protectMetachar Protect Metacharacters
read.columns Read specified columns from a file
qqt Student's t Quantile-Quantile Plot
05.Normalization Topic: Normalization of Microarray Data
06.LinearModels Topic: Linear Models for Microarrays
read.idat Read Illumina expression data directly from IDAT files
selectModel Select Appropriate Linear Model
squeezeVar Squeeze Sample Variances
topSplice Top table of differentially spliced genes or exons
toptable Table of Top Genes from Linear Model Fit
vooma 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
volcanoplot Volcano Plot
voom Transform RNA-Seq Data Ready for Linear Modelling
01.Introduction Introduction to the LIMMA Package
02.Classes Topic: Classes Defined by this Package
arrayWeightsQuick Array Quality Weights
as.data.frame Turn a Microarray Linear Model Object into a Dataframe
barcodeplot Barcode Enrichment Plot
beadCountWeights Bead Count Weights for Illumina BeadChips
avearrays Average Over Replicate Arrays
avedups Average Over Duplicate Spots
classifyTests Multiple Testing Genewise Across Contrasts
designI2M Convert Individual Channel Design Matrix to M-A Format
fitmixture Fit Mixture Model by Non-Linear Least Squares
genas Genuine Association of Gene Expression Profiles
fitted.MArrayLM Fitted Values Method for MArrayLM Fits
geneSetTest Mean-rank Gene Set Test
imageplot3by2 Write Imageplots to Files
intraspotCorrelation Intra-Spot Correlation for Two Color Data
makeUnique Make Values of Character Vector Unique
MAList-class M-value, A-value Expression List - class
normalizeQuantiles Normalize Columns of a Matrix to have the same Quantiles
normalizeForPrintorder Print-Order Normalization
normalizeRobustSpline Normalize Single Microarray Using Shrunk Robust Splines
normalizeVSN Variance Stabilizing Normalization (vsn)
cbind Combine RGList, MAList, EList or EListRaw Objects
changeLog Limma Change Log
EList-class Expression List - class
exprs.MA Extract Log-Expression Matrix from MAList
plotRLDF Plot of regularized linear discriminant functions for microarray data
plotSA Sigma vs A plot for microarray linear model
removeBatchEffect Remove Batch Effect
topRomer Top Gene Set Testing Results from Romer
removeExt Remove Common Extension from File Names
topGO Table of Top GO Terms or Top KEGG Pathways
trimWhiteSpace Trim Leading and Trailing White Space
uniquegenelist Eliminate Duplicate Names from the Gene List
heatdiagram Stemmed Heat Diagram
helpMethods Prompt for Method Help Topics
ids2indices Convert Gene Identifiers to Indices for Gene Sets
lmFit Linear Model for Series of Arrays
imageplot Image Plot of Microarray Statistics
lmscFit Fit Linear Model to Individual Channels of Two-Color Data
normalizeMedianAbsValues Normalize Columns of a Matrix to have the Median Absolute Value
normalizeCyclicLoess Normalize Columns of a Matrix by Cyclic Loess
normexp.signal Expected Signal Given Observed Foreground Under Normal+Exp Model
printorder Identify Order in which Spots were Printed
plotDensities Plot Expression Densities
printtipWeights Sub-array Quality Weights
readHeader Read Header Information from Microarray Raw Data File
readImaGeneHeader Read ImaGene Header Information
subsetting Subset RGList, MAList, EListRaw, EList or MArrayLM Objects
strsplit2 Split Composite Names
weightedLoess Lowess fit with weighting
weighted.median Weighted Median
08.Tests Topic: Hypothesis Testing for Linear Models
07.SingleChannel Topic: Individual Channel Analysis of Two-Color Microarrays
asMatrixWeights asMatrixWeights
auROC Area Under Receiver Operating Curve
blockDiag Block Diagonal Matrix
bwss Between and within sums of squares
contrastAsCoef Reform a Design Matrix to that Contrasts Become Coefficients
contrasts.fit Compute Contrasts from Linear Model Fit
fitFDist Moment Estimation of Scaled F-Distribution
fitGammaIntercept Fit Intercept to Vector of Gamma Distributed Variates
goana Gene Ontology or KEGG Pathway Analysis
kooperberg Kooperberg Model-Based Background Correction for GenePix data
gridr Row and Column Positions on Microarray
LargeDataObject-class Large Data Object - class
mdplot Mean-Difference Plot
merge Merge RGList or MAList Data Objects
nec NormExp Background Correction and Normalization Using Control Probes
normalizeBetweenArrays Normalize Between Arrays
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
plotMA3by2 Write MA-Plots to Files
plotMD Mean-Difference Plot of Expression Data
predFCm Predictive log fold change for microarrays
poolVar Pool Sample Variances with Unequal Variances
residuals.MArrayLM Extract Residuals from MArrayLM Fit
rankSumTestWithCorrelation Two Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For Correlation
QualityWeights Spot Quality Weights
RGList-class Red, Green Intensity List - class
tricubeMovingAverage Moving Average Smoother With Tricube Weights
trigammaInverse Inverse Trigamma Function
write.fit Write MArrayLM Object to a File
zscore Z-score Equivalents
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Date 2016-06-28
License GPL (>=2)
URL http://bioinf.wehi.edu.au/limma
biocViews ExonArray, GeneExpression, Transcription, AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneSetEnrichment, DataImport, Genetics, Bayesian, Clustering, Regression, TimeCourse, Microarray, microRNAArray, mRNAMicroarray, OneChannel, ProprietaryPlatforms, TwoChannel, RNASeq, BatchEffect, MultipleComparison, Normalization, Preprocessing, QualityControl

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