{
  "_id": "6a194240acfb0bcc41dd79be",
  "Package": "arrayQuality",
  "Version": "1.90.0",
  "Date": "2010-04-13",
  "Title": "Assessing array quality on spotted arrays",
  "biocViews": "Microarray,TwoChannel,QualityControl,Visualization",
  "Author": "Agnes Paquet and Jean Yee Hwa Yang <yeehwa@stat.berkeley.edu>",
  "Maintainer": "Agnes Paquet <paquetagnes@yahoo.com>",
  "Description": "Functions for performing print-run and array level quality\nassessment.",
  "License": "LGPL",
  "URL": "http://arrays.ucsf.edu/",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:30:32 UTC",
  "RemoteUrl": "https://github.com/bioc/arrayQuality",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "0e6f4f981e7cdcb5473354c2be61ac8219ca6868",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 06:42:16 UTC",
    "User": "root"
  },
  "MD5sum": "cf13105d6e2ebf27baa603648542a6f3",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "arrayQuality_1.90.0.tar.gz",
  "_fileid": "a11281fba9f9f7b027c8037dd0bd41fb90681e1958b62c19926cd44c3391dd45",
  "_filesize": 13764977,
  "_sha256": "a11281fba9f9f7b027c8037dd0bd41fb90681e1958b62c19926cd44c3391dd45",
  "_created": "2026-05-29T06:42:16.000Z",
  "_published": "2026-05-29T07:37:36.893Z",
  "_jobs": [
    {
      "job": 78451434764,
      "time": 150,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7284737091"
    },
    {
      "job": 78451434784,
      "time": 135,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7284733174"
    },
    {
      "job": 78451434771,
      "time": 169,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7284741512"
    },
    {
      "job": 78451434768,
      "time": 80,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7285536082"
    },
    {
      "job": 78451434775,
      "time": 122,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7285548621"
    },
    {
      "job": 78451025678,
      "time": 206,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284701382"
    },
    {
      "job": 78451434767,
      "time": 107,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284726434"
    },
    {
      "job": 78451434811,
      "time": 95,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7284723716"
    },
    {
      "job": 78451434798,
      "time": 87,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7284722257"
    },
    {
      "job": 78451434786,
      "time": 89,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7284722594"
    }
  ],
  "_bioccheck": {
    "error": 3,
    "warning": 3,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622347361",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/arrayQuality",
  "_commit": {
    "id": "0e6f4f981e7cdcb5473354c2be61ac8219ca6868",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379432
  },
  "_maintainer": {
    "name": "Agnes Paquet",
    "email": "paquetagnes@yahoo.com",
    "login": "agnespaquet",
    "description": "",
    "uuid": 47029899
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.2.0",
      "role": "Depends"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "gridBase",
      "role": "Imports"
    },
    {
      "package": "hexbin",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "marray",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "mclust",
      "role": "Suggests"
    },
    {
      "package": "MEEBOdata",
      "role": "Suggests"
    },
    {
      "package": "HEEBOdata",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.91.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.90.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "microarray",
    "twochannel",
    "qualitycontrol",
    "visualization"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 749,
    "source": "https://www.bioconductor.org/packages/stats/bioc/arrayQuality"
  },
  "_mentions": 10,
  "_searchresults": 10,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/arrayQuality.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "agQuality",
    "controlCodeHeebo",
    "controlCodeMeebo",
    "EMSplit",
    "getSpikeIds",
    "getSpikeIndex",
    "globalQuality",
    "gpQuality",
    "heeboQuality",
    "heeboQualityPlots",
    "HeeboSpotTypes",
    "maQualityPlots",
    "meeboQuality",
    "meeboQualityPlots",
    "MeeboSpotTypes",
    "PRv9mers",
    "PRvQCHyb",
    "qcScore",
    "qualBoxplot",
    "qualityScore",
    "readAgilent",
    "readcontrolCode",
    "readGPR",
    "readSpikeTypes",
    "readSpot",
    "scaleRefTable",
    "slideQuality",
    "spotQuality"
  ],
  "_datasets": [
    {
      "name": "HsReferenceDB",
      "title": "Reference slides for Mouse oligos hybridizations",
      "object": "HsReferenceDB",
      "file": "HsReferenceDB.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "6Hs.073.ambion.ambion.55.40h.gpr",
        "6Hs.074.ambion.ambion.55.40h.gpr",
        "6Hs.075.ambion.ambion.55.40h.2.gpr",
        "6Hs.076.ambion.ambion.55.40h.gpr",
        "6Hs.094.gpr",
        "6Hs.166.gpr",
        "6Hs.167.1.gpr",
        "6Hs.168.gpr",
        "6Hs.169.1.gpr",
        "6Hs.175.gpr",
        "6Hs.176.gpr",
        "6Hs.177.1.gpr",
        "6Hs.178.1.gpr",
        "6Hs.184.1.gpr",
        "6Hs.185.1.gpr",
        "6Hs.186.1.gpr",
        "6Hs.187.1.gpr",
        "6Hs.193.1.gpr",
        "6Hs.194.gpr",
        "6Hs.195.1.gpr",
        "6Hs.243.1.gpr",
        "6Hs.244.1.gpr",
        "Hs_004_186_2.gpr",
        "Hs_004_187_2.gpr",
        "Hs_004_188.gpr",
        "Hs_004_189_1.gpr",
        "Hs_004_235.gpr"
      ],
      "rows": 15,
      "table": true,
      "tojson": true
    },
    {
      "name": "MmDEGenes",
      "title": "Known DE genes for Mouse quality hybridizations.",
      "object": "MmDEGenes",
      "file": "MmDEGenes.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Ref",
        "Name",
        "ID",
        "Median",
        "SD",
        "Grid.R",
        "Grid.C",
        "Spot.R",
        "Spot.C"
      ],
      "rows": 121,
      "table": true,
      "tojson": true
    },
    {
      "name": "MmReferenceDB",
      "title": "Reference slides for Mouse oligos hybridizations",
      "object": "MmReferenceDB",
      "file": "MmReferenceDB.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "10Mm_149.gpr",
        "10Mm_197.gpr",
        "11Mm_196.gpr",
        "11Mm_207.gpr",
        "11Mm_218.gpr",
        "6Mm.163.gpr",
        "6Mm.173.gpr",
        "6Mm.210.gpr",
        "6Mm.224.gpr",
        "6Mm.225.gpr",
        "6Mm.233.gpr",
        "7Mm.112.gpr",
        "7Mm.117.gpr",
        "7Mm.129.gpr",
        "9Mm.095.gpr",
        "9Mm.137.gpr"
      ],
      "rows": 15,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "agQuality",
      "title": "Diagnostic plots and comparative boxplots for general hybridization, Agilent format",
      "topics": [
        "agcontrolCode",
        "agQuality"
      ]
    },
    {
      "page": "globalQuality",
      "title": "Quality measures for general hybridization.",
      "topics": [
        "globalQuality"
      ]
    },
    {
      "page": "gpQuality",
      "title": "Diagnostic plots and comparative boxplots for general hybridization",
      "topics": [
        "gpQuality"
      ]
    },
    {
      "page": "gprDB",
      "title": "Reference slides for Mouse oligos hybridizations",
      "topics": [
        "HsReferenceDB",
        "index.html",
        "MmReferenceDB"
      ]
    },
    {
      "page": "heeboQuality",
      "title": "Diagnostics plots designed for HEEBO set controls",
      "topics": [
        "heeboQuality"
      ]
    },
    {
      "page": "heeboQualityPlots",
      "title": "Qualitative diagnostic plot for general hybridization, specific to HEEBO set.",
      "topics": [
        "heeboQualityPlots"
      ]
    },
    {
      "page": "arrayQuality-internal",
      "title": "Internal arrayQuality functions",
      "topics": [
        "arrayControls",
        "arrayReplicates",
        "arrayScal",
        "BEbin.linear",
        "controlCodeHeebo",
        "controlCodeMeebo",
        "EMSplit",
        "getSpikeIds",
        "getSpikeIndex",
        "gpFlagWt",
        "HeeboSpotTypes",
        "MeeboSpotTypes",
        "outputNormData",
        "qpBEplot.linear",
        "qpBoxplotMeebo",
        "qpDotPlots",
        "qpDotPlotsEEBO",
        "qpDotPlotsMeebo",
        "qpDotPlotsMeebo2",
        "qpHexbin",
        "qpImage",
        "qpMAPlots",
        "qpMisMatchPlot",
        "qpPTLoess",
        "qpS2N",
        "qpS2Neebo",
        "qpS2Nmeebo",
        "qpTiling",
        "quality2HTML",
        "readAllSpikes",
        "replicatesAvariance",
        "setCtlCol",
        "Spike.Cy5vsCy3",
        "Spike.Individual.Sensitivity",
        "Spike.MM.Scatter",
        "Spike.MMplot",
        "Spike.Sensitivity"
      ]
    },
    {
      "page": "maQualityPlots",
      "title": "Qualitative diagnostic plot for general hybridization",
      "topics": [
        "maQualityPlots"
      ]
    },
    {
      "page": "meeboQuality",
      "title": "Diagnostics plots designed for MEEBO set controls",
      "topics": [
        "meeboQuality"
      ]
    },
    {
      "page": "meeboQualityPlots",
      "title": "Qualitative diagnostic plot for general hybridization, specific to MEEBO set.",
      "topics": [
        "meeboQualityPlots"
      ]
    },
    {
      "page": "MmDEGenes",
      "title": "Known DE genes for Mouse quality hybridizations.",
      "topics": [
        "MmDEGenes"
      ]
    },
    {
      "page": "prdata",
      "title": "Example GPR files",
      "topics": [
        "12Mm250.gpr",
        "9Mm137.gpr"
      ]
    },
    {
      "page": "PRv9mers",
      "title": "Print Run Quality version 9mers",
      "topics": [
        "PRv9mers"
      ]
    },
    {
      "page": "PRvQCHyb",
      "title": "Print run Quality version Quality Control Hybridization",
      "topics": [
        "PRvQCHyb"
      ]
    },
    {
      "page": "qcScore",
      "title": "Quality Control score for general hybridization",
      "topics": [
        "qcScore"
      ]
    },
    {
      "page": "qualBoxplot",
      "title": "Comparative boxplot for general hybridization Quality Control",
      "topics": [
        "qualBoxplot"
      ]
    },
    {
      "page": "qualityScore",
      "title": "Quality Control score for general hybridization",
      "topics": [
        "qualityScore"
      ]
    },
    {
      "page": "readAgilent",
      "title": "Extraction of measures from Agilent (.txt) files.",
      "topics": [
        "readAgilent"
      ]
    },
    {
      "page": "readcontrolCode",
      "title": "Control status information",
      "topics": [
        "readcontrolCode"
      ]
    },
    {
      "page": "readGPR",
      "title": "Reading GenePix gpr file",
      "topics": [
        "readGPR"
      ]
    },
    {
      "page": "readSpikeTypes",
      "title": "Read Spike Types File",
      "topics": [
        "readSpikeTypes"
      ]
    },
    {
      "page": "readSpot",
      "title": "Extraction of measures from Spot (.spot) files.",
      "topics": [
        "readSpot"
      ]
    },
    {
      "page": "scaleRefTable",
      "title": "General hybridization quality scaling",
      "topics": [
        "scaleRefTable"
      ]
    },
    {
      "page": "slideQuality",
      "title": "Quality Control statistics for general hybridization",
      "topics": [
        "slideQuality"
      ]
    },
    {
      "page": "spotQuality",
      "title": "Diagnostic plots and comparative boxplots for general hybridization, Spot format",
      "topics": [
        "spotQuality"
      ]
    }
  ],
  "_rundeps": [
    "gridBase",
    "hexbin",
    "lattice",
    "limma",
    "marray",
    "RColorBrewer",
    "statmod"
  ],
  "_score": 3.3010299956639813,
  "_indexed": false,
  "_nocasepkg": "arrayquality",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/arrayQuality",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.90.0",
      "date": "2026-05-29T06:44:37.000Z",
      "distro": "noble",
      "commit": "0e6f4f981e7cdcb5473354c2be61ac8219ca6868",
      "fileid": "27b1f2fa6c1a4defe86f594c2c89907709e2d5d13306d67822127a1948304c88",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622347361"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.90.0",
      "date": "2026-05-29T06:45:10.000Z",
      "distro": "noble",
      "commit": "0e6f4f981e7cdcb5473354c2be61ac8219ca6868",
      "fileid": "d68fe62d9769f64c83863c0deeff77544eaf68f29e66c7523ab70f38bb09fe27",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622347361"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.90.0",
      "date": "2026-05-29T07:36:19.000Z",
      "commit": "0e6f4f981e7cdcb5473354c2be61ac8219ca6868",
      "fileid": "c7dcc81685c22ca32d01d34b7826f614c35e348830001c827c0515fab434cadd",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622347361"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.90.0",
      "date": "2026-05-29T07:36:53.000Z",
      "commit": "0e6f4f981e7cdcb5473354c2be61ac8219ca6868",
      "fileid": "0e919d7d663d0410c40dbb1e3b00dfb445694f219ff2409bd771e4dc72c19039",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622347361"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.90.0",
      "date": "2026-05-29T06:44:25.000Z",
      "commit": "0e6f4f981e7cdcb5473354c2be61ac8219ca6868",
      "fileid": "ce615cad2b8a036b48b2bac084ac5ad6064c4bac9346fa60cc5f54c4e8f9dd41",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622347361"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.90.0",
      "date": "2026-05-29T06:43:48.000Z",
      "commit": "0e6f4f981e7cdcb5473354c2be61ac8219ca6868",
      "fileid": "c802c59643e3c7f8670039ddad4466f02f56360e6dff5372c2188f19b364606a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622347361"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.90.0",
      "date": "2026-05-29T06:43:44.000Z",
      "commit": "0e6f4f981e7cdcb5473354c2be61ac8219ca6868",
      "fileid": "5dcab246991685933ae66c37f3c5a5976f6bd98ce38b6509603ea5cee33acc54",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622347361"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.90.0",
      "date": "2026-05-29T06:43:44.000Z",
      "commit": "0e6f4f981e7cdcb5473354c2be61ac8219ca6868",
      "fileid": "3cf2272a4e05f1d04ff31bd50367ac0096d46296532a5b591a421183d82900a7",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622347361"
    }
  ]
}