{
  "_id": "6ae74f86818c9e3ef6dbbdb2",
  "Package": "a4Base",
  "Type": "Package",
  "Title": "Automated Affymetrix Array Analysis Base Package",
  "Version": "1.61.1",
  "Date": "2026-05-08",
  "Authors@R": "c(\nperson(given = \"Willem\", family = \"Talloen\", role = \"aut\"),\nperson(given = \"Tine\", family = \"Casneuf\", role = \"aut\"),\nperson(given = \"An\", family = \"De Bondt\", role = \"aut\"),\nperson(given = \"Steven\", family = \"Osselaer\", role = \"aut\"),\nperson(given = \"Hinrich\", family = \"Goehlmann\", role = \"aut\"),\nperson(given = \"Willem\", family = \"Ligtenberg\", role = \"aut\"),\nperson(given = \"Tobias\", family = \"Verbeke\", role = \"aut\", email = \"tobias.verbeke@openanalytics.eu\"),\nperson(given = \"Laure\", family = \"Cougnaud\", role = \"cre\", email = \"laure.cougnaud@openanalytics.eu\")\n)",
  "Description": "Base utility functions are available for the Automated\nAffymetrix Array Analysis set of packages.",
  "License": "GPL-3",
  "biocViews": "Microarray",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-08 20:17:21 UTC",
  "RemoteUrl": "https://github.com/bioc/a4Base",
  "RemoteRef": "HEAD",
  "RemoteSha": "a286a267565e66a7eced6ce77cd5e6123d91a2e8",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-01 13:15:51 UTC",
    "User": "root"
  },
  "Author": "Willem Talloen [aut],\nTine Casneuf [aut],\nAn De Bondt [aut],\nSteven Osselaer [aut],\nHinrich Goehlmann [aut],\nWillem Ligtenberg [aut],\nTobias Verbeke [aut],\nLaure Cougnaud [cre]",
  "Maintainer": "Laure Cougnaud <laure.cougnaud@openanalytics.eu>",
  "_user": "bioc",
  "_type": "src",
  "_file": "a4Base_1.61.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/9a72916130194b56089db229b00e51f2692cf79ce9eaedb830bc12aecd8fbe4c",
  "_filesize": 612157,
  "_sha256": "9a72916130194b56089db229b00e51f2692cf79ce9eaedb830bc12aecd8fbe4c",
  "_expires": "2027-02-09T14:41:08.000Z",
  "_created": "2026-11-01T13:15:51.000Z",
  "_published": "2026-11-01T14:41:10.293Z",
  "_upstream": "https://github.com/bioc/a4Base",
  "_status": "success",
  "_maintainer": {
    "name": "Laure Cougnaud",
    "email": "laure.cougnaud@openanalytics.eu",
    "login": "lcougnaud",
    "description": "",
    "uuid": 15339154
  },
  "_jobs": [
    {
      "job": 124859574274,
      "time": 199,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13085551834"
    },
    {
      "job": 124859574299,
      "time": 377,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "13085806442"
    },
    {
      "job": 124859574260,
      "time": 440,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13085937443"
    },
    {
      "job": 124859574222,
      "time": 310,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "13087124061"
    },
    {
      "job": 124859574262,
      "time": 174,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13087337025"
    },
    {
      "job": 124857111537,
      "time": 292,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13084329075"
    },
    {
      "job": 124859574213,
      "time": 167,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13086350578"
    },
    {
      "job": 124859574277,
      "time": 245,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "13084693474"
    },
    {
      "job": 124859574325,
      "time": 253,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "13085033669"
    },
    {
      "job": 124859574332,
      "time": 186,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13085143135"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 2,
    "note": 15
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41308925318",
  "_commit": {
    "id": "a286a267565e66a7eced6ce77cd5e6123d91a2e8",
    "author": "Laure Cougnaud <laure.cougnaud@openanalytics.eu>",
    "committer": "Laure Cougnaud <laure.cougnaud@openanalytics.eu>",
    "message": "update version",
    "time": 1778271441
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "a4Preproc",
      "role": "Depends"
    },
    {
      "package": "a4Core",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "annaffy",
      "role": "Imports"
    },
    {
      "package": "mpm",
      "role": "Imports"
    },
    {
      "package": "genefilter",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "multtest",
      "role": "Imports"
    },
    {
      "package": "glmnet",
      "role": "Imports"
    },
    {
      "package": "gplots",
      "role": "Imports"
    },
    {
      "package": "Cairo",
      "role": "Suggests"
    },
    {
      "package": "ALL",
      "role": "Suggests"
    },
    {
      "package": "hgu95av2.db",
      "role": "Suggests"
    },
    {
      "package": "nlcv",
      "role": "Suggests"
    },
    {
      "package": "gridSVG",
      "role": "Enhances"
    },
    {
      "package": "JavaGD",
      "role": "Enhances"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-19",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.61.1",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.60.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "microarray"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 482,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 728,
    "source": "https://www.bioconductor.org/packages/stats/bioc/a4Base"
  },
  "_searchresults": 9,
  "_abi": {
    "exports": [
      {
        "key": "a4Base::ExpressionSetWithComputation",
        "hash": "f44296604b5ca208"
      },
      {
        "key": "a4Base::fTest",
        "hash": "634c842958bf676e"
      },
      {
        "key": "a4Base::generic:histPvalue",
        "hash": "d5a26da6b8165c6e"
      },
      {
        "key": "a4Base::generic:propDEgenes",
        "hash": "b45aaace576e15af"
      },
      {
        "key": "a4Base::generic:spectralMap",
        "hash": "6cb7f0d9f7e9d360"
      },
      {
        "key": "a4Base::generic:volcanoPlot",
        "hash": "77cb5d80c8e1e45c"
      },
      {
        "key": "a4Base::limma",
        "hash": "9ef1bcdd65782caa"
      },
      {
        "key": "a4Base::tTest",
        "hash": "d2a0cdb97d27856e"
      }
    ],
    "imports": [
      {
        "key": "Biobase::ExpressionSet",
        "hash": "977be3a5f37731d2"
      },
      {
        "key": "Biobase::Versioned",
        "hash": "85bb92eb18e2854f"
      },
      {
        "key": "Biobase::VersionedBiobase",
        "hash": "13a8ac2c79a1328e"
      },
      {
        "key": "Biobase::eSet",
        "hash": "f5a727537605d4e0"
      },
      {
        "key": "a4Core::generic:topTable",
        "hash": "87ea463225155ba9"
      }
    ]
  },
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/a4Base.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "a4palette",
    "addQuantilesColors",
    "boxPlot",
    "combineTwoExpressionSet",
    "computeLogRatio",
    "createExpressionSet",
    "filterVarInt",
    "heatmap.expressionSet",
    "histPvalue",
    "histpvalueplotter",
    "lassoReg",
    "limmaTwoLevels",
    "logReg",
    "plot1gene",
    "plotComb2Samples",
    "plotCombination2genes",
    "plotCombMultSamples",
    "plotLogRatio",
    "probabilitiesPlot",
    "probe2gene",
    "profilesPlot",
    "propDEgenes",
    "propdegenescalculation",
    "replicates",
    "spectralMap",
    "tTest",
    "volcanoPlot",
    "volcanoplotter"
  ],
  "_datasets": [
    {
      "name": "nlcvTT",
      "title": "Data to Demonstrate nlcv and Co Functions",
      "object": "nlcvTT",
      "file": "nlcvTT.rda",
      "class": [
        "nlcv"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "a4palette",
      "title": "Utility function that defines a color palette for use in a4",
      "topics": [
        "a4palette"
      ]
    },
    {
      "page": "addQuantilesColors",
      "title": "Compute quantiles for plotGeneDE function",
      "topics": [
        "addQuantilesColors"
      ]
    },
    {
      "page": "boxPlot",
      "title": "Create a boxplot for a given gene.",
      "topics": [
        "boxPlot"
      ]
    },
    {
      "page": "combineTwoExpressionSet",
      "title": "Combine two ExpressionSet objects",
      "topics": [
        "combineTwoExpressionSet"
      ]
    },
    {
      "page": "computeLogRatio",
      "title": "Summary statistics for gene expression",
      "topics": [
        "computeLogRatio"
      ]
    },
    {
      "page": "createExpressionSet",
      "title": "combine gene expression and phenotype data onto a ExpressionSet object",
      "topics": [
        "createExpressionSet"
      ]
    },
    {
      "page": "ExpressionSetWithComputation-class",
      "title": "Class \"ExpressionSetWithComputation\"",
      "topics": [
        "ExpressionSetWithComputation-class"
      ]
    },
    {
      "page": "filterVarInt",
      "title": "Filtering on Intensity and Variance",
      "topics": [
        "filterVarInt"
      ]
    },
    {
      "page": "heatmap.expressionSet",
      "title": "Image plot of an expressionSet",
      "topics": [
        "heatmap.expressionSet"
      ]
    },
    {
      "page": "histPvalue",
      "title": "Plot the Distribution of P Values",
      "topics": [
        "histPvalue",
        "histPvalue,limma-method",
        "histPvalue,MArrayLM-method",
        "histPvalue,numeric-method"
      ]
    },
    {
      "page": "histpvalueplotter",
      "title": "Workhorse function for the histPvalue function",
      "topics": [
        "histpvalueplotter"
      ]
    },
    {
      "page": "lassoReg",
      "title": "Multiple regression using the Lasso algorithm as implemented in the glmnet package",
      "topics": [
        "lassoReg"
      ]
    },
    {
      "page": "limmaReg",
      "title": "Wrapper for the limma function for the comparison of two groups (two factor levels)",
      "topics": [
        "limmaReg"
      ]
    },
    {
      "page": "limmaTwoLevels",
      "title": "Wrapper for the limma function for the comparison of two groups (two factor levels)",
      "topics": [
        "limmaTwoLevels"
      ]
    },
    {
      "page": "logReg",
      "title": "Logistic regression for predicting the probability to belong to a certain class in binary classification problems",
      "topics": [
        "logReg"
      ]
    },
    {
      "page": "nlcvTT",
      "title": "Data to Demonstrate nlcv and Co Functions",
      "topics": [
        "nlcvTT"
      ]
    },
    {
      "page": "oaColors",
      "title": "Pick One or More OA Colors",
      "topics": [
        "oaColors"
      ]
    },
    {
      "page": "oaPalette",
      "title": "Generate a Palette of OA Colors",
      "topics": [
        "oaPalette"
      ]
    },
    {
      "page": "plot1gene",
      "title": "Create a Profile Plot for a given Gene",
      "topics": [
        "plot1gene"
      ]
    },
    {
      "page": "plotComb2Samples",
      "title": "Plots the correlation in gene expression between two samples",
      "topics": [
        "plotComb2Samples"
      ]
    },
    {
      "page": "plotCombination2genes",
      "title": "Plot a Combination of Two Genes",
      "topics": [
        "plotCombination2genes"
      ]
    },
    {
      "page": "plotCombMultSamples",
      "title": "Plots the correlation in gene expression between more than 2 samples",
      "topics": [
        "plotCombMultSamples"
      ]
    },
    {
      "page": "plotLogRatio",
      "title": "Plot a summary gene expression graph",
      "topics": [
        "plotLogRatio"
      ]
    },
    {
      "page": "probabilitiesPlot",
      "title": "Function to plot the probabilities to belong to a certain class in binary classification problems.",
      "topics": [
        "probabilitiesPlot"
      ]
    },
    {
      "page": "probe2gene",
      "title": "Translate Affymetrix probeset IDs into gene symbols",
      "topics": [
        "probe2gene"
      ]
    },
    {
      "page": "profilesPlot",
      "title": "Plot expression profiles of multiple genes or probesets Plot expression profiles of multiple genes or probesets. Each line depicts a gene, and the color legend can be used to identify the gene.",
      "topics": [
        "profilesPlot"
      ]
    },
    {
      "page": "propDEgenes",
      "title": "Generic function to compute the proportion of differentially expressed genes that are present",
      "topics": [
        "propDEgenes"
      ]
    },
    {
      "page": "propDEgenes-methods",
      "title": "Generic function to compute the proportion of differentially expressed genes that are present",
      "topics": [
        "propDEgenes,limma",
        "propDEgenes,limma-method",
        "propDEgenes,numeric",
        "propDEgenes,numeric-method",
        "propDEgenes-methods"
      ]
    },
    {
      "page": "propdegenescalculation",
      "title": "Estimation of proportion of differentially expressed genes",
      "topics": [
        "propdegenescalculation"
      ]
    },
    {
      "page": "replicates",
      "title": "computes replicates across a vector",
      "topics": [
        "replicates"
      ]
    },
    {
      "page": "spectralMap",
      "title": "Generic function to draw a spectral map, according to JnJ Standards",
      "topics": [
        "spectralMap"
      ]
    },
    {
      "page": "spectralMap-methods",
      "title": "Methods for Function spectralMap according to JnJ Standards",
      "topics": [
        "spectralMap,ExpressionSet,character",
        "spectralMap,ExpressionSet,character-method",
        "spectralMap-methods",
        "volcanoPlot,ExpressionSet,character"
      ]
    },
    {
      "page": "topTable-methods",
      "title": "Methods for topTable",
      "topics": [
        "topTable,fTest",
        "topTable,fTest-method",
        "topTable,limma",
        "topTable,limma-method",
        "topTable,MArrayLM",
        "topTable,MArrayLM-method",
        "topTable,tTest",
        "topTable,tTest-method",
        "topTable-methods"
      ]
    },
    {
      "page": "tTest",
      "title": "Use t Test to Compare Two Groups",
      "topics": [
        "tTest"
      ]
    },
    {
      "page": "volcanoPlot",
      "title": "Draw a Volcano Plot",
      "topics": [
        "volcanoPlot"
      ]
    },
    {
      "page": "volcanoPlot-methods",
      "title": "Draw a Volcano Plot",
      "topics": [
        "volcanoPlot,limma,missing,character",
        "volcanoPlot,limma,missing,character-method",
        "volcanoPlot,limma,missing,missing",
        "volcanoPlot,limma,missing,missing-method",
        "volcanoPlot,numeric,numeric,character",
        "volcanoPlot,numeric,numeric,character-method",
        "volcanoPlot,numeric,numeric,missing",
        "volcanoPlot,numeric,numeric,missing-method",
        "volcanoPlot,tTest,character",
        "volcanoPlot,tTest,missing",
        "volcanoPlot,tTest,missing,character-method",
        "volcanoPlot,tTest,missing,missing-method",
        "volcanoPlot-methods"
      ]
    },
    {
      "page": "volcanoplotter",
      "title": "Workhorse function for the different volcanoPlot methods",
      "topics": [
        "volcanoplotter"
      ]
    }
  ],
  "_rundeps": [
    "a4Core",
    "a4Preproc",
    "annaffy",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocManager",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "cachem",
    "caTools",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "fastmap",
    "foreach",
    "genefilter",
    "generics",
    "glmnet",
    "glue",
    "GO.db",
    "gplots",
    "gtools",
    "httr",
    "IRanges",
    "iterators",
    "jsonlite",
    "KEGGREST",
    "KernSmooth",
    "lattice",
    "lifecycle",
    "limma",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "mpm",
    "multtest",
    "openssl",
    "pkgconfig",
    "png",
    "R6",
    "Rcpp",
    "RcppEigen",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "shape",
    "statmod",
    "survival",
    "sys",
    "vctrs",
    "XML",
    "xtable",
    "XVector"
  ],
  "_score": 2.9542425094393248,
  "_indexed": true,
  "_nocasepkg": "a4base",
  "_universes": [
    "bioc",
    "lcougnaud"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.61.1",
      "date": "2026-11-01T13:40:19.000Z",
      "distro": "resolute",
      "commit": "a286a267565e66a7eced6ce77cd5e6123d91a2e8",
      "fileid": "https://r2.ropensci.org/56440a229721b9f84cfb3aa9f471f3314d8943c29ba09a3888a12452e3a87a17",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308925318"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.61.1",
      "date": "2026-11-01T13:40:56.000Z",
      "distro": "resolute",
      "commit": "a286a267565e66a7eced6ce77cd5e6123d91a2e8",
      "fileid": "https://r2.ropensci.org/c0a0cfd4095ef5fe10fa84e0cf7f0ebbd84af365f43850eca0c7d084eac26f56",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308925318"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.61.1",
      "date": "2026-11-01T14:29:22.000Z",
      "commit": "a286a267565e66a7eced6ce77cd5e6123d91a2e8",
      "fileid": "https://r2.ropensci.org/b17c51fd08a3a17456aa9845aeb6161e8e8eef4ae499de4b12a38573d25da920",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308925318"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.61.1",
      "date": "2026-11-01T14:28:40.000Z",
      "commit": "a286a267565e66a7eced6ce77cd5e6123d91a2e8",
      "fileid": "https://r2.ropensci.org/2696a0a4495ebf5697ddfeaacca82bb3a4a3236f381cde12aa157e2522a794ce",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308925318"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.61.1",
      "date": "2026-11-01T13:38:33.000Z",
      "commit": "a286a267565e66a7eced6ce77cd5e6123d91a2e8",
      "fileid": "https://r2.ropensci.org/b0bae342cfd98b94668258e6b9a06da400e512a623cba167ad15ac7936def021",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308925318"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.61.1",
      "date": "2026-11-01T13:19:18.000Z",
      "commit": "a286a267565e66a7eced6ce77cd5e6123d91a2e8",
      "fileid": "https://r2.ropensci.org/dad8493430f1723d9246221ae90d5596fc6f5609913e7f168f989a4043d8b63c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308925318"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.61.1",
      "date": "2026-11-01T13:19:34.000Z",
      "commit": "a286a267565e66a7eced6ce77cd5e6123d91a2e8",
      "fileid": "https://r2.ropensci.org/98cee8bac93ed0b4ba1ea875bb8b3bb19ca83cb7f247bfd0a54da3aa1cd2f45d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308925318"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.61.1",
      "date": "2026-11-01T13:18:53.000Z",
      "commit": "a286a267565e66a7eced6ce77cd5e6123d91a2e8",
      "fileid": "https://r2.ropensci.org/ce66a54d8b2f4be20301767f3639b42ab125b6b9f1bbbf348f1b261a5a9b8866",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308925318"
    }
  ]
}