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

DOI: 10.18129/B9.bioc.lumi

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Bioconductor version: Release (3.5)

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>, Lei Huang <lhuang at bsd.uchicago.edu>, Gang Feng <g-feng 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

PDF Reference Manual
Text NEWS

Details

biocViews DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel
Version 2.28.0
In Bioconductor since BioC 2.0 (R-2.5) (10.5 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
LinkingTo
Suggests beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer
SystemRequirements
Enhances
URL
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
Build Report

Package Archives

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

Source Package lumi_2.28.0.tar.gz
Windows Binary lumi_2.28.0.zip
Mac OS X 10.11 (El Capitan) lumi_2.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/lumi
Package Short Url http://bioconductor.org/packages/lumi/
Package Downloads Report Download Stats

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