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limma (version 3.28.6)
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
3.28.6
License
GPL (>=2)
Maintainer
Gordon Smyth
Last Published
June 8th, 2016
Functions in limma (3.28.6)
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classifyTests
Multiple Testing Genewise Across Contrasts
exprs.MA
Extract Log-Expression Matrix from MAList
fitFDist
Moment Estimation of Scaled F-Distribution
getEAWP
Extract Basic Data from Expression Data Objects
kooperberg
Kooperberg Model-Based Background Correction for GenePix data
normalizeVSN
Variance Stabilizing Normalization (vsn)
auROC
Area Under Receiver Operating Curve
backgroundCorrect
Correct Intensities for Background
fitmixture
Fit Mixture Model by Non-Linear Least Squares
protectMetachar
Protect Metacharacters
01.Introduction
Introduction to the LIMMA Package
06.LinearModels
Topic: Linear Models for Microarrays
plotWithHighlights
Scatterplot With Highlighting of Special Points
predFCm
Predictive log fold change for microarrays
08.Tests
Topic: Hypothesis Testing for Linear Models
avedups
Average Over Duplicate Spots
gridr
Row and Column Positions on Microarray
removeBatchEffect
Remove Batch Effect
residuals.MArrayLM
Extract Residuals from MArrayLM Fit
diffSplice
Test for Differential Splicing
heatdiagram
Stemmed Heat Diagram
lm.series
Fit Linear Model to Microrray Data by Ordinary Least Squares
MArrayLM-class
Microarray Linear Model Fit - class
as.matrix
Turn a Microarray Data Object into a Matrix
volcanoplot
Volcano Plot
nec
NormExp Background Correction and Normalization Using Control Probes
limmaUsersGuide
View Limma User's Guide
zscore
Z-score Equivalents
ids2indices
Convert Gene Identifiers to Indices for Gene Sets
ma3x3
Two dimensional Moving Averages with 3x3 Window
RGList-class
Red, Green Intensity List - class
makeUnique
Make Values of Character Vector Unique
TestResults-class
Matrix of Test Results - class
fitGammaIntercept
Fit Intercept to Vector of Gamma Distributed Variates
mergeScans
Merge two scans of two-color arrays
normexp.fit.control
Normexp Model Parameter Estimation Aided by Negative Controls
QualityWeights
Spot Quality Weights
changeLog
Limma Change Log
as.data.frame
Turn a Microarray Linear Model Object into a Dataframe
dimnames
Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object
bwss
Between and within sums of squares
read.ilmn
Read Illumina Expression Data
strsplit2
Split Composite Names
bwss.matrix
Between and within sums of squares for matrix
limmaGUI
Graphical User Interface for the limma microarray package
is.fullrank
Check for Full Column Rank
plotMA3by2
Write MA-Plots to Files
printHead
Print Leading Rows of Large Objects
contrastAsCoef
Reform a Design Matrix to that Contrasts Become Coefficients
controlStatus
Set Status of each Spot from List of Spot Types
propTrueNull
Estimate Proportion of True Null Hypotheses
readImaGeneHeader
Read ImaGene Header Information
genas
Genuine Association of Gene Expression Profiles
getSpacing
Get Numerical Spacing
squeezeVar
Squeeze Sample Variances
normalizeBetweenArrays
Normalize Between Arrays
printtipWeights
Sub-array Quality Weights
geneSetTest
Mean-rank Gene Set Test
LargeDataObject-class
Large Data Object - class
rankSumTestWithCorrelation
Two Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For Correlation
read.maimages
Read RGList or EListRaw from Image Analysis Output Files
EList-class
Expression List - class
unwrapdups
Unwrap Duplicate Spot Values from Rows into Columns
arrayWeights
Array Quality Weights
readGAL
Read a GAL file
avereps
Average Over Irregular Replicate Probes
cbind
Combine RGList, MAList, EList or EListRaw Objects
uniquegenelist
Eliminate Duplicate Names from the Gene List
toptable
Table of Top Genes from Linear Model Fit
selectModel
Select Appropriate Linear Model
goana
Gene Ontology or KEGG Pathway Analysis
topGO
Table of Top GO Terms or Top KEGG Pathways
weighted.median
Weighted Median
propexpr
Estimate Proportion of Expressed Probes
readTargets
Read Targets File
tmixture
Estimate Scale Factor in Mixture of t-Distributions
weightedLoess
Lowess fit with weighting
read.columns
Read specified columns from a file
10.GeneSetTests
Topic: Gene Set Tests
PrintLayout
Print Layout - class
blockDiag
Block Diagonal Matrix
designI2M
Convert Individual Channel Design Matrix to M-A Format
contrasts.fit
Compute Contrasts from Linear Model Fit
dim
Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
fitted.MArrayLM
Fitted Values Method for MArrayLM Fits
getLayout
Extract the Print Layout of an Array from the GAL File
03.ReadingData
Topic: Reading Microarray Data from Files
11.RNAseq
Topic: Analysis of RNA-seq Data
09.Diagnostics
Topic: Diagnostics and Quality Assessment
MAList-class
M-value, A-value Expression List - class
logcosh
Logarithm of cosh
lmscFit
Fit Linear Model to Individual Channels of Two-Color Data
modifyWeights
Modify Matrix of Weights By Control Status of Rows
mdplot
Mean-Difference Plot
barcodeplot
Barcode Enrichment Plot
merge
Merge RGList or MAList Data Objects
poolVar
Pool Sample Variances with Unequal Variances
normalizeWithinArrays
Normalize Within Arrays
normalizeQuantiles
Normalize Columns of a Matrix to have the same Quantiles
qqt
Student's t Quantile-Quantile Plot
plotSA
Sigma vs A plot for microarray linear model
modelMatrix
Construct Design Matrix
normexp.fit
Fit Normal+Exp Convolution Model to Observed Intensities
04.Background
Topic: Background Correction
subsetting
Subset RGList, MAList, EListRaw, EList or MArrayLM Objects
plotFB
FB-Plot
topRomer
Top Gene Set Testing Results from Romer
07.SingleChannel
Topic: Individual Channel Analysis of Two-Color Microarrays
plotMA
MA-Plot of Expression Data
02.Classes
Topic: Classes Defined by this Package
printorder
Identify Order in which Spots were Printed
intraspotCorrelation
Intra-Spot Correlation for Two Color Data
05.Normalization
Topic: Normalization of Microarray Data
read.ilmn.targets
Read Illumina Data from a Target Dataframe
arrayWeightsQuick
Array Quality Weights
tricubeMovingAverage
Moving Average Smoother With Tricube Weights
imageplot3by2
Write Imageplots to Files
voom
Transform RNA-Seq Data Ready for Linear Modelling
avearrays
Average Over Replicate Arrays
read.idat
Read Illumina expression data directly from IDAT files
vooma
Convert Mean-Variance Trend to Observation-specific Precision Weights for Microarray Data
romer
Rotation Gene Set Enrichment Analysis
dupcor
Correlation Between Duplicates
trimWhiteSpace
Trim Leading and Trailing White Space
venn
Venn Diagrams
plotlines
plotlines
targetsA2C
Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel
topSplice
Top table of differentially spliced genes or exons
LGchangeLog
LimmaGUI Change Log
ebayes
Empirical Bayes Statistics for Differential Expression
isNumeric
Test for Numeric Argument
plotMD
Mean-Difference Plot of Expression Data
imageplot
Image Plot of Microarray Statistics
alias2Symbol
Convert Gene Aliases to Official Gene Symbols
asMatrixWeights
asMatrixWeights
as.MAList
Convert marrayNorm Object to an MAList Object
beadCountWeights
Bead Count Weights for Illumina BeadChips
gls.series
Fit Linear Model to Microarray Data by Generalized Least Squares
lmFit
Linear Model for Series of Arrays
loessFit
Univariate Lowess With Prior Weights
mrlm
Fit Linear Model to Microrray Data by Robust Regression
normalizeCyclicLoess
Normalize Columns of a Matrix by Cyclic Loess
normexp.signal
Expected Signal Given Observed Foreground Under Normal+Exp Model
plotDensities
Plot Expression Densities
plotSplice
Differential splicing plot
plotPrintTipLoess
MA Plots by Print-Tip Group
normexp.fit.detection.p
Estimate Normexp Model Parameter Using Negative Controls Inferred from Regular Probes
plotRLDF
Plot of regularized linear discriminant functions for microarray data
roast
Rotation Gene Set Tests
trigammaInverse
Inverse Trigamma Function
removeExt
Remove Common Extension from File Names
anova.MAList-method
ANOVA Table - method
camera
Competitive Gene Set Test Accounting for Inter-gene Correlation
decideTests
Multiple Testing Across Genes and Contrasts
normalizeRobustSpline
Normalize Single Microarray Using Shrunk Robust Splines
normalizeMedianAbsValues
Normalize Columns of a Matrix to have the Median Absolute Value
helpMethods
Prompt for Method Help Topics
normalizeForPrintorder
Print-Order Normalization
plotMDS
Multidimensional scaling plot of distances between gene expression profiles
plotExons
Plot exons of differentially expressed gene
readSpotTypes
Read Spot Types File
readHeader
Read Header Information from Microarray Raw Data File
summary
Summaries of Microarray Data Objects
makeContrasts
Construct Matrix of Custom Contrasts
voomWithQualityWeights
Combining observational-level with sample-specific quality weights for RNA-seq analysis
write.fit
Write MArrayLM Object to a File