beadarray

Quality assessment and low-level analysis for Illumina BeadArray data

Bioconductor version: 2.9

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, QualityControl, Preprocessing
Depends	R (>= 2.13.0), Biobase(>= 2.5.5), methods, ggplot2
Imports	BeadDataPackR, limma, AnnotationDbi, reshape2
Suggests	lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db
System Requirements
License	GPL-2
URL
Depends On Me	beadarrayExampleData
Imports Me	arrayQualityMetrics, BeadArrayUseCases
Suggests Me	beadarraySNP, lumi
Version	2.4.2
Since	Bioconductor 1.8 (R-2.3)

Package Downloads

Package Source	beadarray_2.4.2.tar.gz
Windows Binary	beadarray_2.4.2.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	beadarray_2.4.2.tgz
Package Downloads Report	Download Stats

Workflows »

Common Bioconductor workflows include:

Mailing Lists »

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

Hosting provided by Fred Hutchinson Cancer Research Center