To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("beadarray")

In most cases, you don't need to download the package archive at all.

beadarray

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see beadarray.

Quality assessment and low-level analysis for Illumina BeadArray data

Bioconductor version: 3.1

The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

Author: Mark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt Ritchie

Maintainer: Mark Dunning <Mark.Dunning at cruk.cam.ac.uk>

Citation (from within R, enter citation("beadarray")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("beadarray")

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("beadarray")
PDF R Script beadarray.pdf
PDF R Script beadlevel.pdf
PDF R Script beadsummary.pdf
PDF R Script ImageProcessing.pdf
PDF Reference Manual
Text NEWS

Details

biocViews Microarray, OneChannel, Preprocessing, QualityControl, Software
Version 2.18.0
In Bioconductor since BioC 1.8 (R-2.3) (10 years)
License GPL-2
Depends R (>= 2.13.0), BiocGenerics(>= 0.3.2), Biobase(>= 2.17.8), methods, ggplot2
Imports BeadDataPackR, limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, illuminaio
LinkingTo
Suggests lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr
SystemRequirements
Enhances
URL
Depends On Me beadarrayExampleData
Imports Me arrayQualityMetrics, BeadArrayUseCases, blima, epigenomix
Suggests Me beadarraySNP, blimaTestingData, lumi
Build Report

Package Archives

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

Package Source beadarray_2.18.0.tar.gz
Windows Binary beadarray_2.18.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) beadarray_2.18.0.tgz
Mac OS X 10.9 (Mavericks) beadarray_2.18.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/beadarray/tree/release-3.1
Package Short Url http://bioconductor.org/packages/beadarray/
Package Downloads Report Download Stats

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