{ "_id": "6ac8d1acde46216d5edd7e72", "Package": "dyebias", "Title": "The GASSCO method for correcting for slide-dependent\ngene-specific dye bias", "Version": "1.72.0", "Date": "2 March 2016", "Author": "Philip Lijnzaad and Thanasis Margaritis", "Description": "Many two-colour hybridizations suffer from a dye bias that\nis both gene-specific and slide-specific. The former depends on\nthe content of the nucleotide used for labeling; the latter\ndepends on the labeling percentage. The slide-dependency was\nhitherto not recognized, and made addressing the artefact\nimpossible. Given a reasonable number of dye-swapped pairs of\nhybridizations, or of same vs. same hybridizations, both the\ngene- and slide-biases can be estimated and corrected using the\nGASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009),\ndoi:10.1038/msb.2009.21)", "Maintainer": "Philip Lijnzaad ", "License": "GPL-3", "URL": "http://www.holstegelab.nl/publications/margaritis_lijnzaad", "biocViews": "Microarray, TwoChannel, QualityControl, Preprocessing", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:33:49 UTC", "RemoteUrl": "https://github.com/bioc/dyebias", "RemoteRef": "RELEASE_3_23", "RemoteSha": "07a87ca035677e83c4ee2d12d5918655ea2a3877", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-09 11:09:09 UTC", "User": "root" }, "_user": "bioc-release", "_type": "src", "_file": "dyebias_1.72.0.tar.gz", "_fileid": "https://r2.ropensci.org/6e83ae8cc7107b73204291dfff2b96412a51d91eaa1287eb5e9a0721fcbb88ce", "_filesize": 2801974, "_sha256": "6e83ae8cc7107b73204291dfff2b96412a51d91eaa1287eb5e9a0721fcbb88ce", "_expires": "2027-01-17T11:36:08.000Z", "_created": "2026-10-09T11:09:09.000Z", "_published": "2026-10-09T11:36:12.433Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37921490412", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 3, "warning": 4, "note": 17 }, "_upstream": "https://github.com/bioc/dyebias", "_commit": { "id": "07a87ca035677e83c4ee2d12d5918655ea2a3877", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379629 }, "_maintainer": { "name": "Philip Lijnzaad", "email": "plijnzaad@gmail.com", "login": "plijnzaad", "description": "works at the Princess Maxima Centre for Pediatric Oncology, Utrecht, Holland.", "uuid": 11426231 }, "_distro": "resolute", "_jobs": [ { "job": 113791909249, "time": 141, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11612686132" }, { "job": 113791909258, "time": 190, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11611864599" }, { "job": 113791909262, "time": 150, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11612616165" }, { "job": 113791909220, "time": 118, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11613401698" }, { "job": 113791909391, "time": 145, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11612832609" }, { "job": 113790355996, "time": 277, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11612402335" }, { "job": 113791909348, "time": 102, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11612437590" }, { "job": 113791909252, "time": 139, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11612597440" }, { "job": 113791909413, "time": 105, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11612189010" }, { "job": 113791909356, "time": 104, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11612517508" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 1.4.1", "role": "Depends" }, { "package": "marray", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "limma", "role": "Suggests" }, { "package": "convert", "role": "Suggests" }, { "package": "GEOquery", "role": "Suggests" }, { "package": "dyebiasexamples", "role": "Suggests" }, { "package": "methods", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.73.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.72.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "microarray", "twochannel", "qualitycontrol", "preprocessing" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 475, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 664, "source": "https://www.bioconductor.org/packages/stats/bioc/dyebias" }, "_mentions": 1, "_searchresults": 10, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/dyebias.html", "extra/manual.pdf", "LICENSE" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "dyebias.application.subset", "dyebias.apply.correction", "dyebias.boxplot", "dyebias.estimate.iGSDBs", "dyebias.maplot", "dyebias.monotonicity", "dyebias.monotonicityplot", "dyebias.rgplot", "dyebias.trendplot" ], "_help": [ { "page": "dyebias-package", "title": "The GASSCO method for correcting for slide-dependent gene-specific dye bias", "topics": [ "dyebias-package", "dyebias" ] }, { "page": "dyebias.application.subset", "title": "Return a subset of reporters that can be dye bias-corrected reasonably well", "topics": [ "dyebias.application.subset" ] }, { "page": "dyebias.apply.correction", "title": "Perform dye bias correction using the GASSCO method", "topics": [ "dyebias.apply.correction" ] }, { "page": "dyebias.boxplot", "title": "Creates boxplots of the reporters with the strongest dye bias", "topics": [ "dyebias.boxplot" ] }, { "page": "dyebias.estimate.iGSDBs", "title": "Estimate intrinsic gene specific dye biases (part of the GASSCO method)", "topics": [ "dyebias.estimate.iGSDBs" ] }, { "page": "dyebias.monotonicity", "title": "Calculate the degree of monotonicity of the dye bias across the slides. DEPRACATED", "topics": [ "dyebias.monotonicity" ] }, { "page": "dyebias.monotonicityplot", "title": "Show the degree of monotonicity of the dye bias across the slides. DEPRACATED", "topics": [ "dyebias.monotonicityplot" ] }, { "page": "dyebias.rgplot", "title": "Produce scatterplots of the hybridization, with strongest dye biases highlighted.", "topics": [ "dyebias.maplot", "dyebias.rgplot" ] }, { "page": "dyebias.trendplot", "title": "Creates a trend-plot of all reporters, binned by dye bias, with all slides ordered by slide bias.", "topics": [ "dyebias.trendplot" ] } ], "_rundeps": [ "Biobase", "BiocGenerics", "generics", "limma", "marray", "statmod" ], "_vignettes": [ { "source": "dyebias-vignette.Rnw", "filename": "dyebias-vignette.pdf", "title": "dye bias correction", "engine": "utils::Sweave", "headings": [ "Overview", "Installing", "Tuteja et al. (2008)", "Chen et al. (2007)", "Closing remarks", "sessionInfo" ], "created": "2013-11-01 20:08:03", "modified": "2018-09-06 15:51:07", "commits": 3 } ], "_score": 3.3010299956639813, "_indexed": false, "_nocasepkg": "dyebias", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/dyebias", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.72.0", "date": "2026-10-09T11:12:10.000Z", "distro": "resolute", "commit": "07a87ca035677e83c4ee2d12d5918655ea2a3877", "fileid": "https://r2.ropensci.org/24b6cbff9257acbfc8afcf7783337de5e11b33069fa63f91b0a7514c52e3aaa1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37921490412" }, { "r": "4.6.1", "os": "linux", "version": "1.72.0", "date": "2026-10-09T11:11:30.000Z", "distro": "resolute", "commit": "07a87ca035677e83c4ee2d12d5918655ea2a3877", "fileid": "https://r2.ropensci.org/5c060494c945a159030f890e79dcce1cfbffd4a29312e33b5408d2b698e5080f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37921490412" }, { "r": "4.5.3", "os": "mac", "version": "1.72.0", "date": "2026-10-09T11:35:21.000Z", "commit": "07a87ca035677e83c4ee2d12d5918655ea2a3877", "fileid": "https://r2.ropensci.org/194d0f559f9831275b4333691e0165ac6695e0dc28e76baa7f5a3a035bccee9f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37921490412" }, { "r": "4.6.1", "os": "mac", "version": "1.72.0", "date": "2026-10-09T11:26:53.000Z", "commit": "07a87ca035677e83c4ee2d12d5918655ea2a3877", "fileid": "https://r2.ropensci.org/5bdaa68f919c37dcfc1004edc77615b0bdc5cf84afe67e1a5266621842528f61", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37921490412" }, { "r": "4.6.0", "os": "wasm", "version": "1.72.0", "date": "2026-10-09T11:11:11.000Z", "commit": "07a87ca035677e83c4ee2d12d5918655ea2a3877", "fileid": "https://r2.ropensci.org/353c0859dbe30214aa48bd1793508b28844ac7c019f55544bbb39c6f54740525", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37921490412" }, { "r": "4.7.0", "os": "win", "version": "1.72.0", "date": "2026-10-09T11:11:06.000Z", "commit": "07a87ca035677e83c4ee2d12d5918655ea2a3877", "fileid": "https://r2.ropensci.org/4d4c2b8686b40f645d229b62981d908d6648da9ac34626960d7b77c8e5600b4c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37921490412" }, { "r": "4.5.3", "os": "win", "version": "1.72.0", "date": "2026-10-09T11:10:39.000Z", "commit": "07a87ca035677e83c4ee2d12d5918655ea2a3877", "fileid": "https://r2.ropensci.org/18f47b8f373f563c194db8e700b57b93ef2207199194d80cb5892655fc57fe23", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37921490412" }, { "r": "4.6.1", "os": "win", "version": "1.72.0", "date": "2026-10-09T11:10:42.000Z", "commit": "07a87ca035677e83c4ee2d12d5918655ea2a3877", "fileid": "https://r2.ropensci.org/e77e6bb7caed511ef4c743c44dd6e2f153bddaed52a917fee21a655b16775cf8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37921490412" } ] }