dyebias
The GASSCO method for correcting for slide-dependent gene-specific dye bias
Bioconductor version: 3.24 · Package version: 1.73.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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)
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("dyebias")Details
| Maintainer | Philip Lijnzaad <plijnzaad@gmail.com> |
| Author | Philip Lijnzaad and Thanasis Margaritis |
| License | GPL-3 |
| URL | http://www.holstegelab.nl/publications/margaritis_lijnzaad |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Microarray, Preprocessing, QualityControl, Software, TwoChannel |
| Package Short Url | https://bioconductor.org/packages/dyebias/ |
Citation
From within R, enter citation("dyebias"):
Philip Lijnzaad and Thanasis Margaritis. dyebias: The GASSCO method for correcting for slide-dependent gene-specific dye bias. doi:10.18129/B9.bioc.dyebias, R package version 1.73.0, https://bioconductor.org/packages/dyebias.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the 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 (arm64) | dyebias_1.73.0.tgz |
| macOS binary (x86_64) | dyebias_1.73.0.tgz |
Dependencies
Depends: R (>= 1.4.1), marray, Biobase
Suggests: limma, convert, GEOquery, dyebiasexamples, methods
Reverse dependencies
Suggests Me (1): dyebiasexamples