Package: dyebias 1.67.0
Philip Lijnzaad
dyebias: The GASSCO method for correcting for slide-dependent gene-specific dye bias
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)
Authors:
dyebias_1.67.0.tar.gz
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dyebias.pdf |dyebias.html✨
dyebias/json (API)
| # Install 'dyebias' in R: |
| install.packages('dyebias', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:dyebias-1.67.0(bioc 3.21)dyebias-1.66.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarraytwochannelqualitycontrolpreprocessing
Last updated 23 days agofrom:c649c7073e. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 19 2024 |
| R-4.5-win | NOTE | Nov 19 2024 |
| R-4.5-linux | NOTE | Nov 19 2024 |
| R-4.4-win | NOTE | Nov 19 2024 |
| R-4.4-mac | NOTE | Nov 19 2024 |
| R-4.3-win | NOTE | Nov 19 2024 |
| R-4.3-mac | NOTE | Nov 19 2024 |
Exports:dyebias.application.subsetdyebias.apply.correctiondyebias.boxplotdyebias.estimate.iGSDBsdyebias.maplotdyebias.monotonicitydyebias.monotonicityplotdyebias.rgplotdyebias.trendplot
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The GASSCO method for correcting for slide-dependent gene-specific dye bias | dyebias-package dyebias |
| Return a subset of reporters that can be dye bias-corrected reasonably well | dyebias.application.subset |
| Perform dye bias correction using the GASSCO method | dyebias.apply.correction |
| Creates boxplots of the reporters with the strongest dye bias | dyebias.boxplot |
| Estimate intrinsic gene specific dye biases (part of the GASSCO method) | dyebias.estimate.iGSDBs |
| Calculate the degree of monotonicity of the dye bias across the slides. DEPRACATED | dyebias.monotonicity |
| Show the degree of monotonicity of the dye bias across the slides. DEPRACATED | dyebias.monotonicityplot |
| Produce scatterplots of the hybridization, with strongest dye biases highlighted. | dyebias.maplot dyebias.rgplot |
| Creates a trend-plot of all reporters, binned by dye bias, with all slides ordered by slide bias. | dyebias.trendplot |
