DOI: 10.18129/B9.bioc.lumi    

This package is for version 3.6 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see IlluminaHumanMethylation450k.db.

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Bioconductor version: Release (3.6)

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: Pan Du <dupan.mail at>, Lei Huang <lhuang at>, Gang Feng <g-feng at>

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


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biocViews DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel
Version 2.30.0
In Bioconductor since BioC 2.0 (R-2.5) (11 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
Suggests beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer
Depends On Me arrayMvout, ffpeExampleData, iCheck, lumiBarnes, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, MAQCsubset, MAQCsubsetILM, mvoutData, wateRmelon
Imports Me anamiR, ffpe, methyAnalysis, MineICA
Suggests Me beadarray, blima, Harman, methylumi, tigre
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