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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("arrayQualityMetrics")
In most cases, you don't need to download the package archive at all.
arrayQualityMetrics
Quality metrics report for microarray data sets
Bioconductor version: 3.0
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: Audrey Kauffmann <akauffmann.bioinfo at gmail.com>
Citation (from within R,
enter citation("arrayQualityMetrics")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("arrayQualityMetrics")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("arrayQualityMetrics")
| R Script | Advanced topics: Customizing arrayQualityMetrics reports and programmatic processing of the output | |
| R Script | Introduction: microarray quality assessment with arrayQualityMetrics | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Microarray, OneChannel, QualityControl, ReportWriting, Software, TwoChannel |
| Version | 3.22.1 |
| In Bioconductor since | BioC 2.1 (R-2.6) |
| License | LGPL (>= 2) |
| Depends | |
| Imports | affy, affyPLM(>= 1.27.3), beadarray, Biobase, Cairo (>= 1.4-6), genefilter, graphics, grDevices, grid, gridSVG (>= 1.4-3), Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, stats, SVGAnnotation (>= 0.9-0), utils, vsn(>= 3.23.3), XML |
| LinkingTo | |
| Suggests | ALLMLL, CCl4, BiocStyle, knitr |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | arrayQualityMetrics_3.22.1.tar.gz |
| Windows Binary | arrayQualityMetrics_3.22.1.zip |
| Mac OS X 10.6 (Snow Leopard) | arrayQualityMetrics_3.22.1.tgz |
| Mac OS X 10.9 (Mavericks) | arrayQualityMetrics_3.22.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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