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limma (version 3.24.15)
Linear Models for Microarray Data
Description
Data analysis, linear models and differential expression for microarray data.
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3.28.14
3.28.6
3.26.0
3.24.15
3.22.7
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Monthly Downloads
420
Version
3.24.15
License
GPL (>=2)
Maintainer
Gordon Smyth
Last Published
August 5th, 2015
Functions in limma (3.24.15)
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as.MAList
Convert marrayNorm Object to an MAList Object
bwss
Between and within sums of squares
blockDiag
Block Diagonal Matrix
diffSplice
Test for Differential Splicing
as.matrix
Turn a Microarray Data Object into a Matrix
genas
Genuine Association of Gene Expression Profiles
dim
Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
geneSetTest
Mean-rank Gene Set Test
getEAWP
Extract Basic Data from Microarray Data Objects
getLayout
Extract the Print Layout of an Array from the GAL File
limmaUsersGuide
View Limma User's Guide
lm.series
Fit Linear Model to Microrray Data by Ordinary Least Squares
01.Introduction
Introduction to the LIMMA Package
02.Classes
Topic: Classes Defined by this Package
anova.MAList-method
ANOVA Table - method
arrayWeights
Array Quality Weights
barcodeplot
Barcode Enrichment Plot
beadCountWeights
Bead Count Weights for Illumina BeadChips
cbind
Combine RGList, MAList, EList or EListRaw Objects
changeLog
Limma Change Log
fitGammaIntercept
Fit Intercept to Vector of Gamma Distributed Variates
getSpacing
Get Numerical Spacing
fitted.MArrayLM
Fitted Values Method for MArrayLM Fits
gls.series
Fit Linear Model to Microarray Data by Generalized Least Squares
imageplot3by2
Write Imageplots to Files
intraspotCorrelation
Intra-Spot Correlation for Two Color Data
MAList-class
M-value, A-value Expression List - class
mdplot
Mean-Difference Plot
normalizeMedianAbsValues
Normalize Columns of a Matrix to have the Median Absolute Value
normalizeForPrintorder
Print-Order Normalization
rankSumTestWithCorrelation
Two Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For Correlation
read.ilmn.targets
Read Illumina Data from a Target Dataframe
read.maimages
Read RGList or EListRaw from Image Analysis Output Files
read.columns
Read specified columns from a file
squeezeVar
Squeeze Sample Variances
strsplit2
Split Composite Names
trigammaInverse
Inverse Trigamma Function
modelMatrix
Construct Design Matrix
modifyWeights
Modify Matrix of Weights By Control Status of Rows
normexp.fit.detection.p
Estimate Normexp Model Parameter Using Negative Controls Inferred from Regular Probes
predFCm
Predictive log fold change for microarrays
normexp.signal
Expected Signal Given Observed Foreground Under Normal+Exp Model
09.Diagnostics
Topic: Diagnostics and Quality Assessment
printHead
Print Leading Rows of Large Objects
10.GeneSetTests
Topic: Gene Set Tests
asMatrixWeights
asMatrixWeights
auROC
Area Under Receiver Operating Curve
designI2M
Convert Individual Channel Design Matrix to M-A Format
classifyTests
Multiple Testing Genewise Across Contrasts
readTargets
Read Targets File
removeBatchEffect
Remove Batch Effect
removeExt
Remove Common Extension from File Names
residuals.MArrayLM
Extract Residuals from MArrayLM Fit
targetsA2C
Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel
TestResults-class
Matrix of Test Results - class
voomWithQualityWeights
Combining observational-level with sample-specific quality weights for RNA-seq analysis
trimWhiteSpace
Trim Leading and Trailing White Space
weightedLoess
Lowess fit with weighting
zscore
Z-score Equivalents
11.RNAseq
Topic: Analysis of RNA-seq Data
06.LinearModels
Topic: Linear Models for Microarrays
05.Normalization
Topic: Normalization of Microarray Data
alias2Symbol
Convert Gene Aliases to Official Gene Symbols
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
EList-class
Expression List - class
decideTests
Multiple Testing Across Genes and Contrasts
ebayes
Empirical Bayes Statistics for Differential Expression
03.ReadingData
Topic: Reading Microarray Data from Files
04.Background
Topic: Background Correction
avereps
Average Over Irregular Replicate Probes
contrastAsCoef
Reform a Design Matrix to that Contrasts Become Coefficients
backgroundCorrect
Correct Intensities for Background
dimnames
Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object
dupcor
Correlation Between Duplicates
lmscFit
Fit Linear Model to Individual Channels of Two-Color Data
lmFit
Linear Model for Series of Arrays
helpMethods
Prompt for Method Help Topics
heatdiagram
Stemmed Heat Diagram
contrasts.fit
Compute Contrasts from Linear Model Fit
ma3x3
Two dimensional Moving Averages with 3x3 Window
loessFit
Univariate Lowess With Prior Weights
normalizeQuantiles
Normalize Columns of a Matrix to have the same Quantiles
normalizeRobustSpline
Normalize Single Microarray Using Shrunk Robust Splines
plotMA3by2
Write MA-Plots to Files
plotMA
MA-Plot of Expression Data
plotSA
Sigma vs A plot for microarray linear model
plotSplice
Differential splicing plot
propTrueNull
Estimate Proportion of True Null Hypotheses
mergeScans
Merge two scans of two-color arrays
merge
Merge RGList or MAList Data Objects
normalizeCyclicLoess
Normalize Columns of a Matrix by Cyclic Loess
normalizeBetweenArrays
Normalize Between Arrays
plotDensities
Plot Expression Densities
plotExons
Plot exons of differentially expressed gene
subsetting
Subset RGList, MAList, EListRaw, EList or MArrayLM Objects
protectMetachar
Protect Metacharacters
summary
Summaries of Microarray Data Objects
venn
Venn Diagrams
volcanoplot
Volcano Plot
plotWithHighlights
Scatterplot With Highlighting of Special Points
poolVar
Pool Sample Variances with Unequal Variances
printtipWeights
Sub-array Quality Weights
readGAL
Read a GAL file
propexpr
Estimate Proportion of Expressed Probes
readHeader
Read Header Information from Microarray Raw Data File
ids2indices
Convert Gene Identifiers to Indices for Gene Sets
imageplot
Image Plot of Microarray Statistics
kooperberg
Kooperberg Model-Based Background Correction for GenePix data
LargeDataObject-class
Large Data Object - class
makeContrasts
Construct Matrix of Custom Contrasts
makeUnique
Make Values of Character Vector Unique
normalizeVSN
Variance Stabilizing Normalization (vsn)
normalizeWithinArrays
Normalize Within Arrays
plotFB
FB-Plot
plotlines
plotlines
plotMDS
Multidimensional scaling plot of distances between gene expression profiles
plotMD
Mean-Difference Plot of Expression Data
qqt
Student's t Quantile-Quantile Plot
QualityWeights
Spot Quality Weights
read.ilmn
Read Illumina Expression Data
read.idat
Read Illumina expression data directly from IDAT files
romer
Rotation Gene Set Enrichment Analysis
selectModel
Select Appropriate Linear Model
roast
Rotation Gene Set Tests
toptable
Table of Top Genes from Linear Model Fit
tricubeMovingAverage
Moving Average Smoother With Tricube Weights
voom
Transform RNA-Seq Data Ready for Linear Modelling
RGList-class
Red, Green Intensity List - class
vooma
Convert Mean-Variance Trend to Observation-specific Precision Weights for Microarray Data
topGO
Table of Top GO Terms or Top KEGG Pathways
tmixture
Estimate Scale Factor in Mixture of t-Distributions
weighted.median
Weighted Median
write.fit
Write MArrayLM Object to a File
07.SingleChannel
Topic: Individual Channel Analysis of Two-Color Microarrays
08.Tests
Topic: Hypothesis Testing for Linear Models
arrayWeightsQuick
Array Quality Weights
as.data.frame
Turn a Microarray Linear Model Object into a Dataframe
avearrays
Average Over Replicate Arrays
avedups
Average Over Duplicate Spots
exprs.MA
Extract Log-Expression Matrix from MAList
fitFDist
Moment Estimation of Scaled F-Distribution
goana
Gene Ontology or KEGG Pathway Analysis
is.fullrank
Check for Full Column Rank
gridr
Row and Column Positions on Microarray
isNumeric
Test for Numeric Argument
mrlm
Fit Linear Model to Microrray Data by Robust Regression
nec
NormExp Background Correction and Normalization Using Control Probes
normexp.fit
Fit Normal+Exp Convolution Model to Observed Intensities
normexp.fit.control
Normexp Model Parameter Estimation Aided by Negative Controls
plotPrintTipLoess
MA Plots by Print-Tip Group
plotRLDF
Plot of regularized linear discriminant functions for microarray data
PrintLayout
Print Layout - class
printorder
Identify Order in which Spots were Printed
readImaGeneHeader
Read ImaGene Header Information
topRomer
Top Gene Set Testing Results from Romer
readSpotTypes
Read Spot Types File
topSplice
Top table of differentially spliced genes or exons
uniquegenelist
Eliminate Duplicate Names from the Gene List
unwrapdups
Unwrap Duplicate Spot Values from Rows into Columns