Handle Illumina methylation data

Bioconductor version: 2.8

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. Normalization and quality control features for GoldenGate arrays are also included.

Author: Sean Davis, Pan Du, Sven Bilke

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   Reference Manual


biocViews DNAMethylation, TwoChannel, Preprocessing, QualityControl, CpGIsland
Depends R (>= 2.9), Biobase, methods
Imports Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi
Suggests lumi, lattice, limma, xtable, GGHumanMethCancerPanelv1.db
System Requirements
License GPL-2
Depends On Me
Imports Me lumi
Suggests Me IlluminaHumanMethylation450k.db
Version 1.8.0
Since Bioconductor 2.5 (R-2.10)

Package Downloads

Package Source methylumi_1.8.0.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) binary methylumi_1.8.0.tgz
Package Downloads Report Download Stats

Workflows »

Common Bioconductor workflows include:


Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center