arrayQualityMetrics

DOI: 10.18129/B9.bioc.arrayQualityMetrics    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see arrayQualityMetrics.

Quality metrics report for microarray data sets

Bioconductor version: 3.9

This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.

Author: Audrey Kauffmann, Wolfgang Huber

Maintainer: Mike Smith <mike.smith at embl.de>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("arrayQualityMetrics")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("arrayQualityMetrics")

 

PDF	R Script	Advanced topics: Customizing arrayQualityMetrics reports and programmatic processing of the output
PDF	R Script	Introduction: microarray quality assessment with arrayQualityMetrics
PDF		Reference Manual
Text		NEWS

Details

biocViews	Microarray, OneChannel, QualityControl, ReportWriting, Software, TwoChannel
Version	3.40.0
In Bioconductor since	BioC 2.1 (R-2.6) (12 years)
License	LGPL (>= 2)
Depends
Imports	affy, affyPLM(>= 1.27.3), beadarray, Biobase, genefilter, graphics, grDevices, grid, gridSVG (>= 1.4-3), Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, stats, utils, vsn(>= 3.23.3), XML, svglite
LinkingTo
Suggests	ALLMLL, CCl4, BiocStyle, knitr
SystemRequirements
Enhances
URL
BugReports	https://github.com/grimbough/arrayQualityMetrics/issues
Depends On Me	maEndToEnd
Imports Me	EGAD
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	arrayQualityMetrics_3.40.0.tar.gz
Windows Binary	arrayQualityMetrics_3.40.0.zip
Mac OS X 10.11 (El Capitan)	arrayQualityMetrics_3.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/arrayQualityMetrics
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/arrayQualityMetrics
Package Short Url	https://bioconductor.org/packages/arrayQualityMetrics/
Package Downloads Report	Download Stats