Package: dyebias 1.72.0
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_1.72.0.tar.gz
dyebias_1.72.0.zip(r-4.7)dyebias_1.72.0.zip(r-4.6)dyebias_1.72.0.zip(r-4.5)
dyebias_1.72.0.tgz(r-4.6-any)dyebias_1.72.0.tgz(r-4.5-any)
dyebias_1.72.0.tar.gz(r-4.7-any)dyebias_1.72.0.tar.gz(r-4.6-any)
dyebias_1.72.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
dyebias/json (API)
| # Install 'dyebias' in R: |
| install.packages('dyebias', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:dyebias-1.73.0(bioc 3.24)dyebias-1.72.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarraytwochannelqualitycontrolpreprocessing
Last updated from:07a87ca035 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 142 | ||
| linux-devel-x86_64 | NOTE | 219 | ||
| source / vignettes | OK | 220 | ||
| linux-release-x86_64 | NOTE | 182 | ||
| macos-release-arm64 | NOTE | 132 | ||
| macos-oldrel-arm64 | NOTE | 152 | ||
| windows-devel | NOTE | 116 | ||
| windows-release | NOTE | 137 | ||
| windows-oldrel | NOTE | 153 | ||
| wasm-release | OK | 123 |
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 |
