dyebias
This is the development version of dyebias; for the stable release version, see dyebias.
The GASSCO method for correcting for slide-dependent gene-specific dye bias
Bioconductor version: Development (3.24)
Many two-colour hybridizations suffer from a dye bias that is both gene-specific and slide-specific. The former depends on the content of the nucleotide used for labeling; the latter depends on the labeling percentage. The slide-dependency was hitherto not recognized, and made addressing the artefact impossible. Given a reasonable number of dye-swapped pairs of hybridizations, or of same vs. same hybridizations, both the gene- and slide-biases can be estimated and corrected using the GASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009), doi:10.1038/msb.2009.21)
Author: Philip Lijnzaad and Thanasis Margaritis
Maintainer: Philip Lijnzaad <plijnzaad at gmail.com>
citation("dyebias")):
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("dyebias")
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("dyebias")| dye bias correction | R Script | |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | Microarray, Preprocessing, QualityControl, Software, TwoChannel |
| Version | 1.73.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) (17.5 years) |
| License | GPL-3 |
| Depends | R (>= 1.4.1), marray, Biobase |
| Imports | |
| System Requirements | |
| URL | http://www.holstegelab.nl/publications/margaritis_lijnzaad |
See More
| Suggests | limma, convert, GEOquery, dyebiasexamples, methods |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | dyebiasexamples |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | dyebias_1.73.0.tar.gz |
| Windows Binary (x86_64) | dyebias_1.73.0.zip |
| macOS Binary (big-sur-x86_64) | dyebias_1.73.0.tgz |
| macOS Binary (sonoma-arm64) | dyebias_1.73.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/dyebias |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/dyebias |
| Bioc Package Browser | https://code.bioconductor.org/browse/dyebias/ |
| Package Short Url | https://bioconductor.org/packages/dyebias/ |
| Package Downloads Report | Download Stats |