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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("dyebias")
In most cases, you don't need to download the package archive at all.
dyebias
|
This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see dyebias.
The GASSCO method for correcting for slide-dependent gene-specific dye bias
Bioconductor version: 2.12
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 <p.lijnzaad at umcutrecht.nl>
Citation (from within R,
enter citation("dyebias")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("dyebias")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("dyebias")
| R Script | dye bias correction | |
| dyebiasCompleteVignette.pdf | ||
| gassco.pdf | ||
| Reference Manual | ||
| Text | LICENSE |
Details
| biocViews | Microarray, Preprocessing, QualityControl, Software, TwoChannel |
| Version | 1.18.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) (7 years) |
| License | GPL-3 |
| Depends | R (>= 1.4.1), marray, Biobase |
| Imports | |
| LinkingTo | |
| Suggests | limma, convert, GEOquery, dyebiasexamples, methods |
| SystemRequirements | |
| Enhances | |
| URL | http://www.holstegelab.nl/publications/margaritis_lijnzaad |
| Depends On Me | |
| Imports Me | |
| Suggests Me | dyebiasexamples |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | dyebias_1.18.0.tar.gz |
| Windows Binary | dyebias_1.18.0.zip |
| Mac OS X 10.6 (Snow Leopard) | dyebias_1.18.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/dyebias/tree/release-2.12 |
| Package Short Url | http://bioconductor.org/packages/dyebias/ |
| Package Downloads Report | Download Stats |
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