limma

Introduction to the LIMMA Package

Topic: Classes Defined by this Package

Topic: Reading Microarray Data from Files

Topic: Background Correction

Topic: Normalization of Microarray Data

Topic: Linear Models for Microarrays

Topic: Individual Channel Analysis of Two-Color Microarrays

Topic: Hypothesis Testing for Linear Models

Topic: Diagnostics and Quality Assessment

Topic: Gene Set Tests

Topic: Analysis of RNA-seq Data

Expression List (EList) class

Large Data Object - class

Print Layout - class

Matrix of Test Results - class

Convert Gene Aliases to Official Gene Symbols

ANOVA Table - method

Array Quality Weights

Array Quality Weights

asMatrixWeights

Turn a Microarray Linear Model Object into a Dataframe

Convert marrayNorm Object to an MAList Object

Turn a Microarray Data Object into a Matrix

Area Under Receiver Operating Curve

Average Over Replicate Arrays

Average Over Duplicate Spots

Average Over Irregular Replicate Probes

Correct Intensities for Background

Barcode Enrichment Plot

Bead Count Weights for Illumina BeadChips

Block Diagonal Matrix

Between and within sums of squares

Between and within sums of squares for matrix

Competitive Gene Set Test Accounting for Inter-gene Correlation

Combine RGList, MAList, EList or EListRaw Objects

Change Log

Convert Individual Channel Design Matrix to M-A Format

Choose Span for Local-Weighted Regression Smoothing

Genewise Nested F-Tests

Reform a Design Matrix to that Contrasts Become Coefficients

Compute Contrasts from Linear Model Fit

Set Status of each Spot from List of Spot Types

Heatmap of gene expression values

Cumulative Overlap Analysis of Ordered Lists

Multiple Testing Across Genes and Contrasts

Detection P-Values from Negative Controls

Test for Differential Splicing

Retrieve the Dimensions of an RGList, MAList or MArrayLM Object

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

Correlation Between Duplicates

Empirical Bayes Statistics for Differential Expression

Extract Log-Expression Matrix from MAList

Fit Intercept to Vector of Gamma Distributed Variates

Moment Estimation of Scaled F-Distribution

Fit Mixture Model by Non-Linear Least Squares

Fitted Values Method for MArrayLM Fits

Genuine Association of Gene Expression Profiles

Mean-rank Gene Set Test

Extract Basic Data from Expression Data Objects

Get Numerical Spacing

Extract the Print Layout of an Array from the GAL File

Fit Linear Model to Microarray Data by Generalized Least Squares

Gene Ontology or KEGG Pathway Analysis

Row and Column Positions on Microarray

Return the First to Last Part of a Data Object

Stemmed Heat Diagram

Prompt for Method Help Topics

Convert Gene Identifiers to Indices for Gene Sets

Image Plot of Microarray Statistics

Write Imageplots to Files

Intra-Spot Correlation for Two Color Data

Check for Full Column Rank

Test for Numeric Argument

Kooperberg Model-Based Background Correction for GenePix data

View Limma User's Guide

Fit Linear Model to Microrray Data by Ordinary Least Squares

Linear Model for Series of Arrays

Fit Linear Model to Individual Channels of Two-Color Data

Univariate Lowess With Prior Weights

Logarithm of cosh

Log Sum of Exponentials

Two dimensional Moving Averages with 3x3 Window

Construct Matrix of Custom Contrasts

Make Values of Character Vector Unique

M-value, A-value Expression List - class

Microarray Linear Model Fit - class

Mean-Difference Plot

Merge RGList or MAList Data Objects

Merge two scans of two-color arrays

Construct Design Matrix

Modify Matrix of Weights By Control Status of Rows

Fit Linear Model to Microrray Data by Robust Regression

NormExp Background Correction and Normalization Using Control Probes

Normalize Columns of a Matrix by Cyclic Loess

Normalize Columns of a Matrix to have the Median Absolute Value

Normalize Single Microarray Using Shrunk Robust Splines

Variance Stabilizing Normalization (vsn)

Normalize Within Arrays

Normalize Between Arrays

Print-Order Normalization

Normalize Columns of a Matrix to have the same Quantiles

Fit Normal+Exp Convolution Model to Observed Intensities

Normexp Model Parameter Estimation Aided by Negative Controls

Estimate Normexp Model Parameter Using Negative Controls Inferred from Regular Probes

Expected Signal Given Observed Foreground Under Normal+Exp Model

Plot Expression Densities

Differential splicing plot with junctions

Plot exons of differentially expressed gene

FB-Plot

Mean-Difference Plot of Expression Data

Multidimensional scaling plot of distances between gene expression profiles

Plot of regularized linear discriminant functions for microarray data

Sigma vs A plot for microarray linear model

Differential splicing plot

Scatterplot With Highlighting of Special Points

plotlines

MA-Plot of Expression Data

Write MA-Plots to Files

MA Plots by Print-Tip Group

Pool Sample Variances with Unequal Variances

Predictive log fold change for microarrays

Print Leading Rows of Large Objects

Identify Order in which Spots were Printed

Sub-array Quality Weights

Estimate Proportion of True Null Hypotheses

Estimate Proportion of Expressed Probes

Protect Metacharacters

Student's t or Fisher's F Quantile-Quantile Plot

Spot Quality Weights for Spotted Microarrays

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

Read specified columns from a file

Read Illumina expression data directly from IDAT files

Read Illumina Expression Data

Read Illumina Data from a Target Dataframe

Read RGList or EListRaw from Image Analysis Output Files

Read Header Information from Microarray Raw Data File

Read ImaGene Header Information

Read Spot Types File

Read Targets File

Read a GAL file

Remove Batch Effect

Remove Common Extension from File Names

Extract Residuals from MArrayLM Fit

Red, Green Intensity List - class

Rotation Gene Set Tests

Rotation Gene Set Enrichment Analysis

Select Appropriate Linear Model

Squeeze Sample Variances

Split Composite Names

Subset RGList, MAList, EListRaw, EList, MArrayLM or TestResults Objects

Summaries of Microarray Data Objects

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

Estimate Scale Factor in Mixture of t-Distributions

Table of Top GO Terms or Top KEGG Pathways

Top Gene Set Testing Results from Romer

Top table of differentially spliced genes or exons

Table of Top Genes from Linear Model Fit

Moving Average Smoother With Tricube Weights

Inverse Trigamma Function

Trim Leading and Trailing White Space

Eliminate Duplicate Names from the Gene List

Unwrap Duplicate Spot Values from Rows into Columns

Venn Diagrams

Volcano Plot

Transform RNA-Seq Data Ready for Linear Modelling

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

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

LOWESS Smoother with Prior Weights

Weighted Median

Write MArrayLM Object to a File

Weighted Surrogate Variable Analysis

Transform non-normal random deviates to standard normal

Transform t-statistics to standard normal