arrayMvout
This is the development version of arrayMvout; for the stable release version, see arrayMvout.
multivariate outlier detection for expression array QA
Bioconductor version: Development (3.24)
This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate
Author: Z. Gao, A. Asare, R. Wang, V. Carey
Maintainer: V. Carey <stvjc at channing.harvard.edu>
citation("arrayMvout")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("arrayMvout")
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("arrayMvout")| arrayMvout -- multivariate outlier algorithm for expression arrays | R Script | |
| Reference Manual |
Details
| biocViews | Infrastructure, Microarray, QualityControl, Software |
| Version | 1.71.0 |
| In Bioconductor since | BioC 2.3 (R-2.8) (18 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy |
| Imports | mdqc, affyContam, lumi |
| System Requirements | |
| URL |
See More
| Suggests | MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf |
| 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 | arrayMvout_1.71.0.tar.gz |
| Windows Binary (x86_64) | arrayMvout_1.71.0.zip |
| macOS Binary (big-sur-x86_64) | arrayMvout_1.71.0.tgz |
| macOS Binary (sonoma-arm64) | arrayMvout_1.71.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/arrayMvout |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/arrayMvout |
| Bioc Package Browser | https://code.bioconductor.org/browse/arrayMvout/ |
| Package Short Url | https://bioconductor.org/packages/arrayMvout/ |
| Package Downloads Report | Download Stats |