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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("lumi")

To cite this package in a publication, start R and enter:

    citation("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
PDF   Reference Manual

Details

biocViews Microarray, OneChannel, Preprocessing, DNAMethylation, QualityControl, TwoChannel
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
Suggests beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer
System Requirements
License LGPL (>= 2)
URL
Depends On Me arrayMvout, lumiBarnes, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, MAQCsubset, MAQCsubsetILM, mvoutData
Imports Me
Suggests Me beadarray, IlluminaHumanMethylation450k.db, methylumi
Version 2.4.0
Since Bioconductor 2.0 (R-2.5)

Package Downloads

Package Source lumi_2.4.0.tar.gz
Windows Binary lumi_2.4.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary lumi_2.4.0.tgz
Package Downloads Report Download Stats

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