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This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see lumi.

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Bioconductor version: 2.8

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, Gang Feng, Warren Kibbe, Simon Lin

Maintainer: Pan Du <dupan at>

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


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PDF Bioc2007_lumi_presentation.pdf
PDF IlluminaAnnotation.pdf
PDF lumi.pdf
PDF lumi_VST_evaluation.pdf
PDF methylationAnalysis.pdf
PDF   Reference Manual


biocViews DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel
Version 2.4.0
In Bioconductor since BioC 2.0 (R-2.5) (9 years)
License LGPL (>= 2)
Depends R (>= 2.4.0), Biobase(>= 2.5.5), nleqslv
Imports affy(>= 1.23.4), methylumi, annotate, Biobase(>= 2.5.5), mgcv (>= 1.4-0), hdrcde, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, methods
Suggests beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer
Depends On Me arrayMvout, lumiBarnes, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, MAQCsubset, MAQCsubsetILM, mvoutData
Imports Me
Suggests Me beadarray, IlluminaHumanMethylation450k.db, methylumi
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