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arrayQualityMetrics

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see arrayQualityMetrics.

Quality metrics report for microarray data sets


Bioconductor version: 3.20

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>

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

Installation

To install this package, start R (version "4.4") and enter: 


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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Microarray, OneChannel, QualityControl, ReportWriting, Software, TwoChannel
Version 3.62.0
In Bioconductor since BioC 2.1 (R-2.6) (17.5 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
System Requirements
URL
Bug Reports https://github.com/grimbough/arrayQualityMetrics/issues
See More
Suggests ALLMLL, CCl4, BiocStyle, knitr
Linking To
Enhances
Depends On Me maEndToEnd
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package arrayQualityMetrics_3.62.0.tar.gz
Windows Binary (x86_64) arrayQualityMetrics_3.62.0.zip (64-bit only)
macOS Binary (x86_64) arrayQualityMetrics_3.62.0.tgz
macOS Binary (arm64) arrayQualityMetrics_3.62.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/arrayQualityMetrics
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/arrayQualityMetrics
Bioc Package Browser https://code.bioconductor.org/browse/arrayQualityMetrics/
Package Short Url https://bioconductor.org/packages/arrayQualityMetrics/
Package Downloads Report Download Stats