Handle Illumina methylation data

Bioconductor version: Release (2.14)

This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

Author: Sean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla

Maintainer: Sean Davis <sdavis2 at>

To install this package, start R and enter:


To cite this package in a publication, start R and enter:



PDF R Script An Introduction to the methylumi package
PDF R Script Working with Illumina 450k Arrays using methylumi
PDF   Reference Manual


biocViews CpGIsland, DNAMethylation, Preprocessing, QualityControl, Software, TwoChannel
Version 2.10.0
In Bioconductor since BioC 2.5 (R-2.10)
License GPL-2
Depends Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, minfi
Imports Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, BiocGenerics, illuminaio
Suggests lumi, lattice, limma, xtable, IlluminaHumanMethylation27k.db(>= 1.4.4), IlluminaHumanMethylation450k.db, SQN, GenomicRanges, MASS, matrixStats, parallel, rtracklayer, Biostrings, methyAnalysis, FDb.InfiniumMethylation.hg19, TCGAMethylation450k, TxDb.Hsapiens.UCSC.hg19.knownGene, IlluminaHumanMethylation450kanno.ilmn12.hg19, Homo.sapiens, knitr
System Requirements
Depends On Me wateRmelon
Imports Me asmn, ffpe, lumi, methyAnalysis
Suggests Me IlluminaHumanMethylation450k.db

Package Downloads

Package Source methylumi_2.10.0.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) methylumi_2.10.0.tgz
Mac OS X 10.9 (Mavericks)
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