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 2.10 of Bioconductor; for the stable, up-to-date release version, see lumi.

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Bioconductor version: 2.10

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.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 Analyze Illumina Infinium methylation microarray data
PDF Bioc2007_lumi_presentation.pdf
PDF Evaluation of VST algorithm in lumi package
PDF Resolve the inconsistency of Illumina identifiers through nuID
PDF Using lumi A package processing Illumina Microarray
PDF Reference Manual
Text NEWS

Details

biocViews DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel
Version 2.8.0
In Bioconductor since BioC 2.0 (R-2.5) (9 years)
License LGPL (>= 2)
Depends R (>= 2.10), methylumi(>= 1.7.4), Biobase(>= 2.5.5), nleqslv
Imports affy(>= 1.23.4), methylumi, genoset, GenomicRanges, IRanges, rtracklayer, annotate, Biobase(>= 2.5.5), mgcv (>= 1.4-0), hdrcde, 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, lumiBarnes, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, MAQCsubset, MAQCsubsetILM, mvoutData
Imports Me ffpe
Suggests Me beadarray, methylumi, tigre, virtualArray
Build Report

Package Archives

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

Package Source lumi_2.8.0.tar.gz
Windows Binary lumi_2.8.0.zip
Mac OS X 10.6 (Snow Leopard)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/lumi/tree/release-2.10
Package Short Url http://bioconductor.org/packages/lumi/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

AltStyle によって変換されたページ (->オリジナル) /