lumi

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Bioconductor version: Development (3.0)

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: Pan Du <dupan.mail at gmail.com>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("lumi")

To cite this package in a publication, start R and enter:

    citation("lumi")

Documentation

PDF R Script Analyze Illumina Infinium methylation microarray data
PDF R Script Evaluation of VST algorithm in lumi package
PDF R Script Resolve the inconsistency of Illumina identifiers through nuID
PDF R Script Using lumi A package processing Illumina Microarray
PDF   Reference Manual
Text   NEWS

Details

biocViews DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel
Version 2.17.0
In Bioconductor since BioC 2.0 (R-2.5)
License LGPL (>= 2)
Depends R (>= 2.10), Biobase(>= 2.5.5)
Imports affy(>= 1.23.4), methylumi(>= 2.3.2), GenomicFeatures, GenomicRanges, annotate, Biobase(>= 2.5.5), 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
System Requirements
URL
Depends On Me arrayMvout, ffpeExampleData, lumiBarnes, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, MAQCsubset, MAQCsubsetILM, mvoutData, wateRmelon
Imports Me ffpe, methyAnalysis, MineICA
Suggests Me beadarray, methylumi, tigre, virtualArray

Package Downloads

Package Source lumi_2.17.0.tar.gz
Windows Binary lumi_2.17.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) lumi_2.17.0.tgz
Mac OS X 10.9 (Mavericks)
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