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This is the development version of lumi; for the stable release version, see lumi.

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Bioconductor version: Development (3.20)

The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.

Author: Pan Du, Richard Bourgon, Gang Feng, Simon Lin

Maintainer: Lei Huang <lhuang1998 at>

Citation (from within R, enter citation("lumi")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


Reference Manual PDF


biocViews DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel
Version 2.57.0
In Bioconductor since BioC 2.0 (R-2.5) (17 years)
License LGPL (>= 2)
Depends R (>= 2.10), Biobase(>= 2.5.5)
Imports affy(>= 1.23.4), methylumi(>= 2.3.2), GenomicFeatures, GenomicRanges, annotate, lattice, mgcv (>= 1.4-0), nleqslv, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, stats4, methods
System Requirements
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Suggests beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer
Linking To
Depends On Me iCheck, wateRmelon, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, ffpeExampleData, lumiBarnes, MAQCsubset, mvoutData
Imports Me arrayMvout, ffpe, MineICA
Suggests Me beadarray, blima, Harman, methylumi, tigre, maGUI
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package lumi_2.57.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) lumi_2.57.0.tgz
macOS Binary (arm64) lumi_2.57.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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