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

DOI: 10.18129/B9.bioc.arrayQualityMetrics

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>

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

Installation

To install this package, start R (version "3.6") 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 3.40.0

In Bioconductor since BioC 2.1 (R-2.6) (16.5 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

Suggests ALLMLL, CCl4, BiocStyle, knitr

Linking To

Enhances

Depends On Me maEndToEnd

Imports Me EGAD

Suggests Me

Links To Me

Build Report Build Report