To install this package, start R and enter:

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

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

beadarray

Quality assessment and low-level analysis for Illumina BeadArray data

Bioconductor version: Release (2.14)

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:

source("http://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 2.14.1
In Bioconductor since BioC 1.8 (R-2.3)
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
Suggests lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr
System Requirements
URL
Depends On Me beadarrayExampleData
Imports Me arrayQualityMetrics, BeadArrayUseCases, epigenomix
Suggests Me beadarraySNP, lumi

Package Archives

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

Package Source beadarray_2.14.1.tar.gz
Windows Binary beadarray_2.14.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) beadarray_2.14.1.tgz
Mac OS X 10.9 (Mavericks) beadarray_2.14.1.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center