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 is the development version of lumi; for the stable release version, see lumi.

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Bioconductor version: Development (3.4)

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>

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 IlluminaAnnotation.pdf
PDF lumi.pdf
PDF lumi_VST_evaluation.pdf
PDF methylationAnalysis.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel
Version 2.25.0
In Bioconductor since BioC 2.0 (R-2.5) (9 years)
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
LinkingTo
Suggests beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer
SystemRequirements
Enhances
URL
Depends On Me arrayMvout, iCheck, wateRmelon
Imports Me 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.

Package Source lumi_2.25.0.tar.gz
Windows Binary lumi_2.25.0.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
Package Short Url http://bioconductor.org/packages/lumi/
Package Downloads Report Download Stats

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