lumi

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Bioconductor version: Release (2.7)

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

To install this package, start R and enter:

source("http:///biocLite.R")
biocLite("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

Reference Manual

Details

biocViews	Microarray, OneChannel, Preprocessing, DNAMethylation, QualityControl, TwoChannel
Depends	R, Biobase
Imports	affy, methylumi, annotate, Biobase, mgcv, hdrcde, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, methods
Suggests	beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer
System Requirements
License	LGPL (>= 2)
URL
Depends On Me	arrayMvout
Imports Me
Suggests Me	beadarray
Version	2.2.1

Package Downloads

Package Source	lumi_2.2.1.tar.gz
Windows Binary	lumi_2.2.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	lumi_2.2.1.tgz
Package Downloads Report	Download Stats