To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("lumi")

In most cases, you don't need to download the package archive at all.

lumi

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 northwestern.edu>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("lumi")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("lumi")

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

Details

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
LinkingTo
Suggests	beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer
SystemRequirements
Enhances
URL
Depends On Me	arrayMvout, lumiBarnes, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, MAQCsubset, MAQCsubsetILM, mvoutData
Imports Me
Suggests Me	beadarray, IlluminaHumanMethylation450k.db, methylumi
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	lumi_2.4.0.tar.gz
Windows Binary	lumi_2.4.0.zip
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/lumi/tree/release-2.8
Package Short Url	http://bioconductor.org/packages/lumi/
Package Downloads Report	Download Stats