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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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Version

Monthly Downloads

565

Version

3.24.15

License

GPL (>=2)

Maintainer

Gordon Smyth

Last Published

February 15th, 2017

Functions in limma (3.24.15)

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