lumi
This is the development version of lumi; for the stable release version, see lumi.
All Bioconductor versions of lumi
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
Bioconductor version: 3.24 · Package version: 2.65.0
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 gmail.com>
Citation
From within R, enter citation("lumi"):
Pan Du, Richard Bourgon, Gang Feng, Simon Lin. lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays. doi:10.18129/B9.bioc.lumi, R package version 2.65.0, https://bioconductor.org/packages/lumi.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("lumi")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 2.65.0 |
| License | LGPL (>= 2) |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 2.5 or earlier (R-2.10) (16 years) |
| Downloads rank | 213 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel |
| Package Short Url | https://bioconductor.org/packages/lumi/ |
Documentation
| Reference Manual | |
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | lumi_2.65.0.tar.gz |
| Windows binary (x86_64) | lumi_2.65.0.zip |
| macOS binary (arm64) | lumi_2.65.0.tgz |
| macOS binary (x86_64) | lumi_2.65.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/lumi |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/lumi |
| Package Downloads Report | Download Stats |
Dependencies
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
Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer
Reverse dependencies
Depends On Me (9): ffpeExampleData, iCheck, lumiBarnes, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, MAQCsubset, mvoutData, wateRmelon
Imports Me (2): arrayMvout, ffpe
Suggests Me (6): beadarray, blima, Harman, maGUI, methylumi, tigre