dyebias
The GASSCO method for correcting for slide-dependent gene-specific dye bias
Bioconductor version: Release (3.17)
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")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.60.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) (14.5 years) |
| License | GPL-3 |
| Depends | R (>= 1.4.1), marray, Biobase |
| Imports | |
| Linking To | |
| Suggests | limma, convert, GEOquery, dyebiasexamples, methods |
| System Requirements | |
| Enhances | |
| URL | http://www.holstegelab.nl/publications/margaritis_lijnzaad |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | dyebiasexamples |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | dyebias_1.60.0.tar.gz |
| Windows Binary | dyebias_1.60.0.zip |
| macOS Binary (x86_64) | dyebias_1.60.0.tgz |
| macOS Binary (arm64) | dyebias_1.60.0.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 |