limma package - RDocumentation

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

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

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

limma (version 3.28.14)

Linear Models for Microarray Data

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Functions in limma (3.28.14)