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  "Date": "2025-02-04",
  "Title": "Classes and Methods for \"Class Comparison\" Problems on\nMicroarrays",
  "Authors@R": "person(given = c(\"Kevin\", \"R.\"),\nfamily = \"Coombes\",\nrole = c(\"aut\", \"cre\"),\nemail = \"krc@silicovore.com\")",
  "Description": "Defines the classes used for \"class comparison\" problems\nin the OOMPA project (<http://oompa.r-forge.r-project.org/>).\nClass comparison includes tests for differential expression;\nsee Simon's book for details on typical problem types.",
  "License": "Apache License (== 2.0)",
  "LazyLoad": "yes",
  "biocViews": "Microarray, DifferentialExpression, MultipleComparisons",
  "URL": "http://oompa.r-forge.r-project.org/",
  "Repository": "https://r-forge.r-universe.dev",
  "Date/Publication": "2026-07-29 15:40:19 UTC",
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    "countSignificant",
    "cutoffSignificant",
    "Dudoit",
    "dwil",
    "hist",
    "image",
    "likelihoodBum",
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    "MultiTtest",
    "MultiTtestPaired",
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    "multiTukey",
    "MultiWilcoxonTest",
    "plot",
    "probDiff",
    "rankSum",
    "Sam",
    "selectSignificant",
    "show",
    "SingleGroup",
    "SmoothTtest",
    "summary",
    "TNoM",
    "TwoGroupStats",
    "update"
  ],
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    {
      "page": "cc00-0-Bum-class",
      "title": "Class \"Bum\"",
      "topics": [
        "Bum",
        "Bum-class",
        "countSignificant,Bum-method",
        "cutoffSignificant,Bum-method",
        "hist,Bum-method",
        "image,Bum-method",
        "likelihoodBum",
        "selectSignificant,Bum-method",
        "summary,Bum-method"
      ]
    },
    {
      "page": "cc00-1-BumSummary-class",
      "title": "Class \"BumSummary\"",
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        "BumSummary",
        "BumSummary-class",
        "show,BumSummary-method"
      ]
    },
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      "page": "cc04-0-Dudoit-class",
      "title": "Class \"Dudoit\"",
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        "countSignificant,Dudoit-method",
        "cutoffSignificant,Dudoit-method",
        "Dudoit",
        "Dudoit-class",
        "plot,Dudoit,missing-method",
        "selectSignificant,Dudoit-method"
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    },
    {
      "page": "cc02-1-dwil",
      "title": "Wilcoxon Density Function",
      "topics": [
        "dwil"
      ]
    },
    {
      "page": "cc03-0-MultiLinearModel-class",
      "title": "Class \"MultiLinearModel\"",
      "topics": [
        "anova,MultiLinearModel-method",
        "as.data.frame,MultiLinearModel-method",
        "hist,MultiLinearModel-method",
        "MultiLinearModel",
        "MultiLinearModel-class",
        "multiTukey",
        "plot,MultiLinearModel,ANY-method",
        "plot,MultiLinearModel,missing-method",
        "summary,MultiLinearModel-method"
      ]
    },
    {
      "page": "cc01-0-MultiTtest-class",
      "title": "Class \"MultiTtest\"",
      "topics": [
        "as.data.frame,MultiTtest-method",
        "hist,MultiTtest-method",
        "MultiTtest",
        "MultiTtest-class",
        "plot,MultiTtest,ANY-method",
        "plot,MultiTtest,missing-method",
        "summary,MultiTtest-method"
      ]
    },
    {
      "page": "cc02-0-MultiWilcoxonTest-class",
      "title": "Class \"MultiWilcoxonTest\"",
      "topics": [
        "countSignificant,MultiWilcoxonTest-method",
        "cutoffSignificant,MultiWilcoxonTest-method",
        "hist,MultiWilcoxonTest-method",
        "MultiWilcoxonTest",
        "MultiWilcoxonTest-class",
        "plot,MultiWilcoxonTest,missing-method",
        "probDiff,MultiWilcoxonTest-method",
        "selectSignificant,MultiWilcoxonTest-method",
        "summary,MultiWilcoxonTest-method"
      ]
    },
    {
      "page": "cc02-2-rankSum",
      "title": "Wilcoxon Rank-Sum Statistic",
      "topics": [
        "rankSum"
      ]
    },
    {
      "page": "cc06-0-Sam-class",
      "title": "Class \"Sam\"",
      "topics": [
        "countSignificant,Sam-method",
        "plot,Sam,missing-method",
        "Sam",
        "Sam-class",
        "selectSignificant,Sam-method",
        "summary,Sam-method"
      ]
    },
    {
      "page": "cc06-1-SamSummary-class",
      "title": "Class \"SamSummary\"",
      "topics": [
        "SamSummary",
        "SamSummary-class",
        "show,SamSummary-method"
      ]
    },
    {
      "page": "cc00-2-significant-method",
      "title": "Generic Methods for Significance",
      "topics": [
        "countSignificant",
        "countSignificant,ANY-method",
        "countSignificant-method",
        "cutoffSignificant",
        "cutoffSignificant,ANY-method",
        "cutoffSignificant-method",
        "probDiff",
        "probDiff,ANY-method",
        "probDiff-method",
        "selectSignificant",
        "selectSignificant,ANY-method",
        "selectSignificant-method"
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      "title": "Class \"SingleGroup\"",
      "topics": [
        "as.data.frame,SingleGroup-method",
        "plot,SingleGroup,missing-method",
        "print,SingleGroup-method",
        "show,SingleGroup-method",
        "SingleGroup",
        "SingleGroup-class",
        "summary,SingleGroup-method"
      ]
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        "plot,SmoothTtest,missing-method",
        "SmoothTtest",
        "SmoothTtest-class",
        "summary,SmoothTtest-method"
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        "MultiTtestUnequal",
        "MultiTtestUnequal-class",
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      "source": "oompa-cc.Rnw",
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        "Permutation based methods",
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      "created": "2014-02-10 15:51:10",
      "modified": "2014-05-05 19:51:49",
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