arrayQualityMetrics
This is the released version of arrayQualityMetrics; for the devel version, see arrayQualityMetrics.
Quality metrics report for microarray data sets
Bioconductor version: Release (3.23)
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 [aut], Wolfgang Huber [aut], Hugo Gruson [cre]
Maintainer: Hugo Gruson <hugo.gruson at embl.de>
citation("arrayQualityMetrics")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | HTML | R Script |
| Introduction: microarray quality assessment with arrayQualityMetrics | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Microarray, OneChannel, QualityControl, ReportWriting, Software, TwoChannel |
| Version | 3.68.0 |
| In Bioconductor since | BioC 2.1 (R-2.6) (19 years) |
| License | LGPL (>= 2) |
| Depends | |
| Imports | affy, affyPLM(>= 1.27.3), beadarray, Biobase, genefilter, graphics, grDevices, grid, gridSVG (>= 1.4-3), Hmisc, hwriter, jsonlite, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, stats, utils, vsn(>= 3.23.3), XML, svglite |
| System Requirements | |
| URL | https://github.com/Huber-group-EMBL/arrayQualityMetrics |
| Bug Reports | https://github.com/Huber-group-EMBL/arrayQualityMetrics/issues |
See More
| Suggests | ALLMLL, CCl4, BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| 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_3.68.0.tar.gz |
| Windows Binary (x86_64) | arrayQualityMetrics_3.68.0.zip |
| macOS Binary (big-sur-x86_64) | arrayQualityMetrics_3.68.0.tgz |
| macOS Binary (sonoma-arm64) | arrayQualityMetrics_3.68.0.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 |