{
  "_id": "6a1a74c61d7bb097a09d1927",
  "Package": "arrayMvout",
  "Title": "multivariate outlier detection for expression array QA",
  "Version": "1.70.0",
  "Author": "Z. Gao, A. Asare, R. Wang, V. Carey",
  "Description": "This package supports the application of diverse quality\nmetrics to AffyBatch instances, summarizing these metrics via\nPCA, and then performing parametric outlier detection on the\nPCs to identify aberrant arrays with a fixed Type I error rate",
  "Maintainer": "V. Carey <stvjc@channing.harvard.edu>",
  "License": "Artistic-2.0",
  "LazyLoad": "yes",
  "biocViews": "Infrastructure, Microarray, QualityControl",
  "RoxygenNote": "7.1.1",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:33:30 UTC",
  "RemoteUrl": "https://github.com/bioc/arrayMvout",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "5586fa40895612119eed169592e7bb52498d08b5",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 06:56:17 UTC",
    "User": "root"
  },
  "MD5sum": "315c0476c52785dd63c010a9370a397c",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "arrayMvout_1.70.0.tar.gz",
  "_fileid": "0ded9af27819cdb4d6680aded0c3f2611f73fa95abba65061151ceaf3ec01e2a",
  "_filesize": 696236,
  "_sha256": "0ded9af27819cdb4d6680aded0c3f2611f73fa95abba65061151ceaf3ec01e2a",
  "_created": "2026-05-29T06:56:17.000Z",
  "_published": "2026-05-30T05:25:26.349Z",
  "_jobs": [
    {
      "job": 78626308033,
      "time": 301,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7305657980"
    },
    {
      "job": 78626308217,
      "time": 620,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7285053900"
    },
    {
      "job": 78626308239,
      "time": 621,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7285053876"
    },
    {
      "job": 78626308274,
      "time": 303,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7285950155"
    },
    {
      "job": 78626308248,
      "time": 301,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7285957966"
    },
    {
      "job": 78626308022,
      "time": 515,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284902669"
    },
    {
      "job": 78626308224,
      "time": 307,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284975751"
    },
    {
      "job": 78626308124,
      "time": 404,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7305666114"
    },
    {
      "job": 78626308230,
      "time": 513,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7285027495"
    },
    {
      "job": 78626308218,
      "time": 531,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7285032016"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 3,
    "note": 13
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622699593",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/arrayMvout",
  "_commit": {
    "id": "5586fa40895612119eed169592e7bb52498d08b5",
    "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": 1777379610
  },
  "_maintainer": {
    "name": "V. Carey",
    "email": "stvjc@channing.harvard.edu",
    "login": "vjcitn",
    "description": "Professor of Medicine, Channing Division of Network Medicine, Mass General Brigham, Harvard Medical School.",
    "uuid": 4624066
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.6.0",
      "role": "Depends"
    },
    {
      "package": "tools",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Depends"
    },
    {
      "package": "parody",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "affy",
      "role": "Depends"
    },
    {
      "package": "mdqc",
      "role": "Imports"
    },
    {
      "package": "affyContam",
      "role": "Imports"
    },
    {
      "package": "lumi",
      "role": "Imports"
    },
    {
      "package": "MAQCsubset",
      "role": "Suggests"
    },
    {
      "package": "mvoutData",
      "role": "Suggests"
    },
    {
      "package": "lumiBarnes",
      "role": "Suggests"
    },
    {
      "package": "affyPLM",
      "role": "Suggests"
    },
    {
      "package": "affydata",
      "role": "Suggests"
    },
    {
      "package": "hgu133atagcdf",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.71.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.70.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "infrastructure",
    "microarray",
    "qualitycontrol"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 536,
    "source": "https://www.bioconductor.org/packages/stats/bioc/arrayMvout"
  },
  "_mentions": 3,
  "_searchresults": 13,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/arrayMvout.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "ArrayOutliers",
    "plot",
    "show"
  ],
  "_datasets": [
    {
      "name": "afxsubDEG",
      "title": "Multivariate outlier detection based on PCA of QA statistics",
      "object": "afxsubDEG",
      "file": "afxsubDEG.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "fig3map",
      "title": "Multivariate outlier detection based on PCA of QA statistics",
      "object": "fig3map",
      "file": "fig3map.rda",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "ilmQA",
      "title": "Multivariate outlier detection based on PCA of QA statistics",
      "object": "ilmQA",
      "file": "ilmQA.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "mean",
        "standard deviation",
        "detection rate(0.01)",
        "distance to sample mean"
      ],
      "rows": 19,
      "table": true,
      "tojson": true
    },
    {
      "name": "itnQA",
      "title": "Multivariate outlier detection based on PCA of QA statistics",
      "object": "itnQA",
      "file": "itnQA.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "avgBG",
        "SF",
        "Present",
        "HSACO7",
        "GAPDH",
        "NUSE",
        "RLE",
        "RLE_IQR",
        "RNAslope"
      ],
      "rows": 507,
      "table": true,
      "tojson": true
    },
    {
      "name": "maqcQA",
      "title": "Multivariate outlier detection based on PCA of QA statistics",
      "object": "maqcQA",
      "file": "maqcQA.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "X",
        "celfile",
        "avgBG",
        "SF",
        "Present",
        "HSACO7",
        "GAPDH",
        "NUSE",
        "RLE",
        "RLE_IQR",
        "RNAslope"
      ],
      "rows": 120,
      "table": true,
      "tojson": true
    },
    {
      "name": "s12cDEG",
      "title": "Multivariate outlier detection based on PCA of QA statistics",
      "object": "s12cDEG",
      "file": "s12cDEG.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "spikQA",
      "title": "Multivariate outlier detection based on PCA of QA statistics",
      "object": "spikQA",
      "file": "spikQA.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "avgBG",
        "SF",
        "Present",
        "HSACO7",
        "GAPDH",
        "NUSE",
        "RLE",
        "RLE_IQR",
        "RNAslope"
      ],
      "rows": 12,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ArrayOutliers",
      "title": "Multivariate outlier detection based on PCA of QA statistics",
      "topics": [
        "afxsubDEG",
        "afxsubQC",
        "ArrayOutliers",
        "fig3map",
        "ILM1",
        "ilmQA",
        "itnQA",
        "maqcQA",
        "s12c",
        "s12cDEG",
        "s12cQC",
        "spikQA"
      ]
    },
    {
      "page": "ArrayOutliers-methods",
      "title": "ArrayOutliers - wrapper for platform-specific multivariate outlier detection for expression arrays",
      "topics": [
        "ArrayOutliers,AffyBatch,numeric,ANY-method",
        "ArrayOutliers,ANY,missing,missing-method",
        "ArrayOutliers,data.frame,numeric,ANY-method",
        "ArrayOutliers,LumiBatch,numeric,ANY-method",
        "ArrayOutliers-methods"
      ]
    },
    {
      "page": "arrOutStruct-class",
      "title": "Class \"arrOutStruct\" container for ArrayOutliers output",
      "topics": [
        "arrOutStruct-class",
        "plot,arrOutStruct,ANY-method",
        "show,arrOutStruct-method"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "affy",
    "affyContam",
    "affydata",
    "affyio",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "base64",
    "beanplot",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocManager",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "bumphunter",
    "cachem",
    "cigarillo",
    "cli",
    "clipr",
    "cluster",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "DelayedMatrixStats",
    "digest",
    "dir.expiry",
    "doRNG",
    "dplyr",
    "farver",
    "fastmap",
    "FDb.InfiniumMethylation.hg19",
    "filelock",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "genefilter",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "GEOquery",
    "ggplot2",
    "glue",
    "gtable",
    "h5mread",
    "HDF5Array",
    "hms",
    "httr",
    "httr2",
    "illuminaio",
    "IRanges",
    "isoband",
    "iterators",
    "jsonlite",
    "KEGGREST",
    "KernSmooth",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "lumi",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mclust",
    "mdqc",
    "memoise",
    "methylumi",
    "mgcv",
    "mime",
    "minfi",
    "multtest",
    "nleqslv",
    "nlme",
    "nor1mix",
    "openssl",
    "org.Hs.eg.db",
    "parody",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "preprocessCore",
    "prettyunits",
    "progress",
    "purrr",
    "quadprog",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "readr",
    "rentrez",
    "reshape",
    "reshape2",
    "restfulr",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "Rhtslib",
    "rjson",
    "rlang",
    "rngtools",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "scrime",
    "selectr",
    "Seqinfo",
    "siggenes",
    "snow",
    "SparseArray",
    "sparseMatrixStats",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "TxDb.Hsapiens.UCSC.hg19.knownGene",
    "tzdb",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "arrayMvout.Rnw",
      "filename": "arrayMvout.pdf",
      "title": "arrayMvout -- multivariate outlier algorithm for expression arrays",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 20:06:09",
      "modified": "2020-12-08 14:06:38",
      "commits": 3
    }
  ],
  "_score": 3.892094602690481,
  "_indexed": false,
  "_nocasepkg": "arraymvout",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/arrayMvout",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.70.0",
      "date": "2026-05-29T07:03:11.000Z",
      "distro": "noble",
      "commit": "5586fa40895612119eed169592e7bb52498d08b5",
      "fileid": "f0aa64561a43025af0ee5773bc863753878b3d1c5d7fb822ff7b06a57a5efe72",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622699593"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.70.0",
      "date": "2026-05-29T07:03:29.000Z",
      "distro": "noble",
      "commit": "5586fa40895612119eed169592e7bb52498d08b5",
      "fileid": "a957e71a09310a28b0d14b34cda8f4680fa1beab39ab8919c6d3c940ce0398e5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622699593"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.70.0",
      "date": "2026-05-29T07:58:28.000Z",
      "commit": "5586fa40895612119eed169592e7bb52498d08b5",
      "fileid": "77c1bc6389853c4b48c22b284be5e54743b59f0049c5e31145c98bebec0e06ed",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622699593"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.70.0",
      "date": "2026-05-29T07:58:54.000Z",
      "commit": "5586fa40895612119eed169592e7bb52498d08b5",
      "fileid": "15585974b71d1b84bb226ff6df4b46a0fb78f761a103d50ea3f8ce183ed16663",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622699593"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.70.0",
      "date": "2026-05-29T07:02:15.000Z",
      "commit": "5586fa40895612119eed169592e7bb52498d08b5",
      "fileid": "ff703ed241e1a4901afdc47f239b7b7a761a5049cf02988eb94d6c208c6e615d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622699593"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.70.0",
      "date": "2026-05-30T05:21:21.000Z",
      "commit": "5586fa40895612119eed169592e7bb52498d08b5",
      "fileid": "666506fad1cddda26a7c584647824821710db911163a86123f847a3f6ccdfdbd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622699593"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.70.0",
      "date": "2026-05-29T07:01:14.000Z",
      "commit": "5586fa40895612119eed169592e7bb52498d08b5",
      "fileid": "c3c5b7b544b10ae907c76067f49fbe4ef6cbf0d4c7fc8e7af735c783ddce0ab2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622699593"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.70.0",
      "date": "2026-05-29T07:01:14.000Z",
      "commit": "5586fa40895612119eed169592e7bb52498d08b5",
      "fileid": "abf52fb2e9ce7820ade1abf84faf8e548f559d8ca2edfe084a66bb7b8f1d2014",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622699593"
    }
  ]
}