lumi

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Bioconductor version: Release (2.11)

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		Bioc2007_lumi_presentation.pdf
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	2.10.0
In Bioconductor since	BioC 2.0 (R-2.5)
License	LGPL (>= 2)
Depends	R (>= 2.10), Biobase(>= 2.5.5), nleqslv
Imports	affy(>= 1.23.4), methylumi(>= 2.3.2), annotate, Biobase(>= 2.5.5), lattice, mgcv (>= 1.4-0), hdrcde, 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
Imports Me	ffpe, methyAnalysis
Suggests Me	beadarray, methylumi, tigre, virtualArray