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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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Version

Monthly Downloads

127

Version

3.28.6

License

GPL (>=2)

Maintainer

Gordon Smyth

Last Published

February 15th, 2017

Functions in limma (3.28.6)

Multiple Testing Genewise Across Contrasts

Extract Log-Expression Matrix from MAList

Moment Estimation of Scaled F-Distribution

Extract Basic Data from Expression Data Objects

Kooperberg Model-Based Background Correction for GenePix data

Variance Stabilizing Normalization (vsn)

Area Under Receiver Operating Curve

backgroundCorrect

Correct Intensities for Background

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

Predictive log fold change for microarrays

Topic: Hypothesis Testing for Linear Models

Average Over Duplicate Spots

Row and Column Positions on Microarray

removeBatchEffect

Remove Batch Effect

residuals.MArrayLM

Extract Residuals from MArrayLM Fit

Test for Differential Splicing

Stemmed Heat Diagram

Fit Linear Model to Microrray Data by Ordinary Least Squares

Microarray Linear Model Fit - class

Turn a Microarray Data Object into a Matrix

NormExp Background Correction and Normalization Using Control Probes

limmaUsersGuide

View Limma User's Guide

Z-score Equivalents

Convert Gene Identifiers to Indices for Gene Sets

Two dimensional Moving Averages with 3x3 Window

Red, Green Intensity List - class

Make Values of Character Vector Unique

TestResults-class

Matrix of Test Results - class

fitGammaIntercept

Fit Intercept to Vector of Gamma Distributed Variates

Merge two scans of two-color arrays

normexp.fit.control

Normexp Model Parameter Estimation Aided by Negative Controls

Spot Quality Weights

Limma Change Log

Turn a Microarray Linear Model Object into a Dataframe

Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object

Between and within sums of squares

Read Illumina Expression Data

Split Composite Names

Between and within sums of squares for matrix

Graphical User Interface for the limma microarray package

Check for Full Column Rank

Write MA-Plots to Files

Print Leading Rows of Large Objects

Reform a Design Matrix to that Contrasts Become Coefficients

Set Status of each Spot from List of Spot Types

Estimate Proportion of True Null Hypotheses

readImaGeneHeader

Read ImaGene Header Information

Genuine Association of Gene Expression Profiles

Get Numerical Spacing

Squeeze Sample Variances

normalizeBetweenArrays

Normalize Between Arrays

printtipWeights

Sub-array Quality Weights

Mean-rank Gene Set Test

LargeDataObject-class

Large Data Object - class

rankSumTestWithCorrelation

Two Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For Correlation

Read RGList or EListRaw from Image Analysis Output Files

Expression List - class

Unwrap Duplicate Spot Values from Rows into Columns

Array Quality Weights

Read a GAL file

Average Over Irregular Replicate Probes

Combine RGList, MAList, EList or EListRaw Objects

Eliminate Duplicate Names from the Gene List

Table of Top Genes from Linear Model Fit

Select Appropriate Linear Model

Gene Ontology or KEGG Pathway Analysis

Table of Top GO Terms or Top KEGG Pathways

weighted.median

Weighted Median

Estimate Proportion of Expressed Probes

Read Targets File

Estimate Scale Factor in Mixture of t-Distributions

Lowess fit with weighting

Read specified columns from a file

10.GeneSetTests

Topic: Gene Set Tests

Print Layout - class

Block Diagonal Matrix

Convert Individual Channel Design Matrix to M-A Format

Compute Contrasts from Linear Model Fit

Retrieve the Dimensions of an RGList, MAList or MArrayLM Object

fitted.MArrayLM

Fitted Values Method for MArrayLM Fits

Extract the Print Layout of an Array from the GAL File

Topic: Reading Microarray Data from Files

Topic: Analysis of RNA-seq Data

Topic: Diagnostics and Quality Assessment

M-value, A-value Expression List - class

Logarithm of cosh

Fit Linear Model to Individual Channels of Two-Color Data

Modify Matrix of Weights By Control Status of Rows

Mean-Difference Plot

Barcode Enrichment Plot

Merge RGList or MAList Data Objects

Pool Sample Variances with Unequal Variances

normalizeWithinArrays

Normalize Within Arrays

normalizeQuantiles

Normalize Columns of a Matrix to have the same Quantiles

Student's t Quantile-Quantile Plot

Sigma vs A plot for microarray linear model

Construct Design Matrix

Fit Normal+Exp Convolution Model to Observed Intensities

Topic: Background Correction

Subset RGList, MAList, EListRaw, EList or MArrayLM Objects

Top Gene Set Testing Results from Romer

07.SingleChannel

Topic: Individual Channel Analysis of Two-Color Microarrays

MA-Plot of Expression Data

Topic: Classes Defined by this Package

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

Write Imageplots to Files

Transform RNA-Seq Data Ready for Linear Modelling

Average Over Replicate Arrays

Read Illumina expression data directly from IDAT files

Convert Mean-Variance Trend to Observation-specific Precision Weights for Microarray Data

Rotation Gene Set Enrichment Analysis

Correlation Between Duplicates

Trim Leading and Trailing White Space

Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel

Top table of differentially spliced genes or exons

LimmaGUI Change Log

Empirical Bayes Statistics for Differential Expression

Test for Numeric Argument

Mean-Difference Plot of Expression Data

Image Plot of Microarray Statistics

Convert Gene Aliases to Official Gene Symbols

asMatrixWeights

asMatrixWeights

Convert marrayNorm Object to an MAList Object

beadCountWeights

Bead Count Weights for Illumina BeadChips

Fit Linear Model to Microarray Data by Generalized Least Squares

Linear Model for Series of Arrays

Univariate Lowess With Prior Weights

Fit Linear Model to Microrray Data by Robust Regression

normalizeCyclicLoess

Normalize Columns of a Matrix by Cyclic Loess

Expected Signal Given Observed Foreground Under Normal+Exp Model

Plot Expression Densities

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

Plot of regularized linear discriminant functions for microarray data

Rotation Gene Set Tests

trigammaInverse

Inverse Trigamma Function

Remove Common Extension from File Names

anova.MAList-method

ANOVA Table - method

Competitive Gene Set Test Accounting for Inter-gene Correlation

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

Prompt for Method Help Topics

normalizeForPrintorder

Print-Order Normalization

Multidimensional scaling plot of distances between gene expression profiles

Plot exons of differentially expressed gene

Read Spot Types File

Read Header Information from Microarray Raw Data File

Summaries of Microarray Data Objects

Construct Matrix of Custom Contrasts

voomWithQualityWeights

Combining observational-level with sample-specific quality weights for RNA-seq analysis

Write MArrayLM Object to a File