beadarray

Quality assessment and low-level analysis for Illumina BeadArray data

Bioconductor version: Release (2.11)

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 cancer.org.uk>

To install this package, start R and enter:

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

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

    citation("beadarray")

Documentation

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	2.8.1
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, BiocGenerics, reshape2
Suggests	lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra
System Requirements
URL
Depends On Me	beadarrayExampleData
Imports Me	arrayQualityMetrics, BeadArrayUseCases
Suggests Me	beadarraySNP, lumi

Package Downloads

Package Source	beadarray_2.8.1.tar.gz
Windows Binary	beadarray_2.8.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard)	beadarray_2.8.1.tgz
Package Downloads Report	Download Stats

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