{
 "about": {
  "method": "qpcr-efficiency and geNorm M",
  "ruling": "docs/board/memos/2026-10-13-cso-qpcr-efficiency-reference-stability.md",
  "origin": "Self-constructed Cq tables",
  "tolerances": {
   "slope, intercept, R^2, interval ends, E, efficiency %": "1e-9 relative",
   "geNorm V and M": "1e-9 relative",
   "states, reasons, counts, dropped levels and samples, ranking order": "exact"
  },
  "recordedOn": "2026-10-13",
  "script": "pipeline/assay-analyser/oracles/qpcr_efficiency.py",
  "scriptSha256": "8d5ef5a60194dc12477a2cf80f5573cb85b6325a8501293c48c511252a2f5a7a",
  "helper": {
   "script": "pipeline/assay-analyser/oracles/stage_a_oracle.py",
   "sha256": "492d85ca2fa6750db80b1c64214fd4a0b13cd4c588267244f6262c504c73e3e8"
  },
  "environment": {
   "image": "ghcr.io/biotechmat/drybench/oracle-env:11b8a5e4456df7eb@sha256:7e69891ca1d9f24838660e0a9887bdb654ce7771d2f2ac7e7275e9b1eb3b6a09",
   "r": "R version 4.4.3 (2025-02-28)",
   "packages": {
    "jsonlite": "2.0.0"
   },
   "python": "3.11.15",
   "numpy": "2.0.2",
   "scipy": "1.13.1",
   "recordedOn": "2026-10-13",
   "cpu": "AMD EPYC 9V45 96-Core Processor",
   "cpuClass": "x86-64-v3",
   "simd": [
    "SSSE3",
    "SSE41",
    "POPCNT",
    "SSE42",
    "AVX",
    "F16C",
    "FMA3",
    "AVX2"
   ],
   "openblasCore": "Haswell",
   "threads": 1
  },
  "crossCheck": {
   "tool": "R stats lm and confint (efficiency), sd (geNorm pairwise V)",
   "version": "R version 4.4.3 (2025-02-28)",
   "script": "pipeline/assay-analyser/oracles/r/qpcr_efficiency.R",
   "scriptSha256": "0ee53205ee773342b36e588134a0976e9c90ce792d9596d25d93e59028f620a7",
   "ran": true,
   "agreement": "every slope, intercept and interval end, and every pairwise SD, within 1e-9 relative; the script stops otherwise"
  }
 },
 "oracle": {
  "engine": "Python fractions and 60-digit decimal (least squares on level means, geNorm), scipy.stats.t for the quantile"
 },
 "efficiency": [
  {
   "name": "e01-perfect",
   "about": "Quantities 1 to 1e-4, Cq = 15 + 3.321928094887362 k, triplicates: E = 2, R^2 = 1, a zero-width interval",
   "convention": "quantity",
   "rows": [
    {
     "assay": "ACTB",
     "quantity": "1",
     "technical": "1",
     "cq": 15.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "ACTB",
     "quantity": "1",
     "technical": "2",
     "cq": 15.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "ACTB",
     "quantity": "1",
     "technical": "3",
     "cq": 15.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "ACTB",
     "quantity": "0.1",
     "technical": "1",
     "cq": 18.32192809488736,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "ACTB",
     "quantity": "0.1",
     "technical": "2",
     "cq": 18.32192809488736,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "ACTB",
     "quantity": "0.1",
     "technical": "3",
     "cq": 18.32192809488736,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "ACTB",
     "quantity": "0.01",
     "technical": "1",
     "cq": 21.643856189774723,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "ACTB",
     "quantity": "0.01",
     "technical": "2",
     "cq": 21.643856189774723,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "ACTB",
     "quantity": "0.01",
     "technical": "3",
     "cq": 21.643856189774723,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "ACTB",
     "quantity": "0.001",
     "technical": "1",
     "cq": 24.965784284662085,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "ACTB",
     "quantity": "0.001",
     "technical": "2",
     "cq": 24.965784284662085,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "ACTB",
     "quantity": "0.001",
     "technical": "3",
     "cq": 24.965784284662085,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "ACTB",
     "quantity": "0.0001",
     "technical": "1",
     "cq": 28.287712379549447,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "ACTB",
     "quantity": "0.0001",
     "technical": "2",
     "cq": 28.287712379549447,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "ACTB",
     "quantity": "0.0001",
     "technical": "3",
     "cq": 28.287712379549447,
     "status": "measured",
     "excluded": false
    }
   ],
   "expected": {
    "status": "fitted",
    "levels": [
     {
      "quantity": 1.0,
      "log10Quantity": 0.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 15.0,
      "residual": 0.0
     },
     {
      "quantity": 0.1,
      "log10Quantity": -1.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 18.32192809488736,
      "residual": 0.0
     },
     {
      "quantity": 0.01,
      "log10Quantity": -2.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 21.643856189774723,
      "residual": 0.0
     },
     {
      "quantity": 0.001,
      "log10Quantity": -3.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 24.965784284662085,
      "residual": 0.0
     },
     {
      "quantity": 0.0001,
      "log10Quantity": -4.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 28.287712379549447,
      "residual": 0.0
     }
    ],
    "dropped": [],
    "slope": -3.3219280948873617,
    "intercept": 15.0,
    "rSquared": 1.0,
    "amplification": 2.0000000000000004,
    "efficiencyPercent": 100.00000000000003,
    "aboveDoubling": false,
    "carryable": true,
    "carriedValue": 2.0,
    "cqRange": [
     15.0,
     28.287712379549447
    ],
    "interval": {
     "slopeLow": -3.3219280948873617,
     "slopeHigh": -3.3219280948873617,
     "eLow": 2.0000000000000004,
     "eHigh": 2.0000000000000004,
     "df": 3
    }
   }
  },
  {
   "name": "e02-ninety",
   "about": "Slope -1/log10(1.9) with +/-0.05 at levels 2 and 4",
   "convention": "quantity",
   "rows": [
    {
     "assay": "GAPDH",
     "quantity": "1",
     "technical": "1",
     "cq": 18.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "GAPDH",
     "quantity": "1",
     "technical": "2",
     "cq": 18.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "GAPDH",
     "quantity": "1",
     "technical": "3",
     "cq": 18.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "GAPDH",
     "quantity": "0.1",
     "technical": "1",
     "cq": 21.637398,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "GAPDH",
     "quantity": "0.1",
     "technical": "2",
     "cq": 21.637398,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "GAPDH",
     "quantity": "0.1",
     "technical": "3",
     "cq": 21.637398,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "GAPDH",
     "quantity": "0.01",
     "technical": "1",
     "cq": 25.174795,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "GAPDH",
     "quantity": "0.01",
     "technical": "2",
     "cq": 25.174795,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "GAPDH",
     "quantity": "0.01",
     "technical": "3",
     "cq": 25.174795,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "GAPDH",
     "quantity": "0.001",
     "technical": "1",
     "cq": 28.712193,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "GAPDH",
     "quantity": "0.001",
     "technical": "2",
     "cq": 28.712193,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "GAPDH",
     "quantity": "0.001",
     "technical": "3",
     "cq": 28.712193,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "GAPDH",
     "quantity": "0.0001",
     "technical": "1",
     "cq": 32.34959,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "GAPDH",
     "quantity": "0.0001",
     "technical": "2",
     "cq": 32.34959,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "GAPDH",
     "quantity": "0.0001",
     "technical": "3",
     "cq": 32.34959,
     "status": "measured",
     "excluded": false
    }
   ],
   "expected": {
    "status": "fitted",
    "levels": [
     {
      "quantity": 1.0,
      "log10Quantity": 0.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 18.0,
      "residual": -0.02000020000000049
     },
     {
      "quantity": 0.1,
      "log10Quantity": -1.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 21.637398,
      "residual": 0.04000030000000088
     },
     {
      "quantity": 0.01,
      "log10Quantity": -2.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 25.174795,
      "residual": -2.0000000020559127e-07
     },
     {
      "quantity": 0.001,
      "log10Quantity": -3.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 28.712193,
      "residual": -0.03999970000000026
     },
     {
      "quantity": 0.0001,
      "log10Quantity": -4.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 32.34959,
      "residual": 0.019999800000000078
     }
    ],
    "dropped": [],
    "slope": -3.5773974999999996,
    "intercept": 18.020000200000002,
    "rSquared": 0.9999687455386016,
    "amplification": 1.9034120605854237,
    "efficiencyPercent": 90.34120605854237,
    "aboveDoubling": false,
    "carryable": true,
    "carriedValue": 1.9034120605854237,
    "cqRange": [
     18.0,
     32.34959
    ],
    "interval": {
     "slopeLow": -3.6141452246221264,
     "slopeHigh": -3.540649775377873,
     "eLow": 1.890995942761742,
     "eHigh": 1.9161699903039031,
     "df": 3
    }
   }
  },
  {
   "name": "e03-two-levels",
   "about": "Two levels: refused",
   "convention": "quantity",
   "rows": [
    {
     "assay": "B2M",
     "quantity": "1",
     "technical": "1",
     "cq": 15,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "B2M",
     "quantity": "1",
     "technical": "2",
     "cq": 15.1,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "B2M",
     "quantity": "1",
     "technical": "3",
     "cq": 14.9,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "B2M",
     "quantity": "0.1",
     "technical": "1",
     "cq": 18.3,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "B2M",
     "quantity": "0.1",
     "technical": "2",
     "cq": 18.4,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "B2M",
     "quantity": "0.1",
     "technical": "3",
     "cq": 18.2,
     "status": "measured",
     "excluded": false
    }
   ],
   "expected": {
    "status": "refused",
    "reason": "too-few-levels",
    "levels": [
     {
      "quantity": 1.0,
      "log10Quantity": 0.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 15.0
     },
     {
      "quantity": 0.1,
      "log10Quantity": -1.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 18.3
     }
    ],
    "dropped": []
   }
  },
  {
   "name": "e04-three-levels",
   "about": "Three levels: value shown, interval withheld",
   "convention": "quantity",
   "rows": [
    {
     "assay": "B2M",
     "quantity": "1",
     "technical": "1",
     "cq": 15,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "B2M",
     "quantity": "1",
     "technical": "2",
     "cq": 15.1,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "B2M",
     "quantity": "1",
     "technical": "3",
     "cq": 14.9,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "B2M",
     "quantity": "0.1",
     "technical": "1",
     "cq": 18.3,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "B2M",
     "quantity": "0.1",
     "technical": "2",
     "cq": 18.4,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "B2M",
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     "technical": "3",
     "cq": 18.2,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "B2M",
     "quantity": "0.01",
     "technical": "1",
     "cq": 21.6,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "B2M",
     "quantity": "0.01",
     "technical": "2",
     "cq": 21.7,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "B2M",
     "quantity": "0.01",
     "technical": "3",
     "cq": 21.5,
     "status": "measured",
     "excluded": false
    }
   ],
   "expected": {
    "status": "fitted",
    "levels": [
     {
      "quantity": 1.0,
      "log10Quantity": 0.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 15.0,
      "residual": 1.9737298215558337e-16
     },
     {
      "quantity": 0.1,
      "log10Quantity": -1.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 18.3,
      "residual": -3.9474596431116675e-16
     },
     {
      "quantity": 0.01,
      "log10Quantity": -2.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 21.6,
      "residual": 1.9737298215558337e-16
     }
    ],
    "dropped": [],
    "slope": -3.3000000000000003,
    "intercept": 15.0,
    "rSquared": 1.0,
    "amplification": 2.009233002565047,
    "efficiencyPercent": 100.9233002565047,
    "aboveDoubling": true,
    "carryable": false,
    "carriedValue": null,
    "cqRange": [
     15.0,
     21.6
    ],
    "interval": {
     "withheld": "three-levels"
    }
   }
  },
  {
   "name": "e05-positive-slope",
   "about": "Cq rising with quantity: refused",
   "convention": "quantity",
   "rows": [
    {
     "assay": "HPRT",
     "quantity": "1",
     "technical": "1",
     "cq": 25,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "HPRT",
     "quantity": "1",
     "technical": "2",
     "cq": 25.1,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "HPRT",
     "quantity": "1",
     "technical": "3",
     "cq": 24.9,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "HPRT",
     "quantity": "0.1",
     "technical": "1",
     "cq": 22,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "HPRT",
     "quantity": "0.1",
     "technical": "2",
     "cq": 22.1,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "HPRT",
     "quantity": "0.1",
     "technical": "3",
     "cq": 21.9,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "HPRT",
     "quantity": "0.01",
     "technical": "1",
     "cq": 19,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "HPRT",
     "quantity": "0.01",
     "technical": "2",
     "cq": 19.1,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "HPRT",
     "quantity": "0.01",
     "technical": "3",
     "cq": 18.9,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "HPRT",
     "quantity": "0.001",
     "technical": "1",
     "cq": 16,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "HPRT",
     "quantity": "0.001",
     "technical": "2",
     "cq": 16.1,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "HPRT",
     "quantity": "0.001",
     "technical": "3",
     "cq": 15.9,
     "status": "measured",
     "excluded": false
    }
   ],
   "expected": {
    "status": "refused",
    "reason": "slope-not-negative",
    "levels": [
     {
      "quantity": 1.0,
      "log10Quantity": 0.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 25.0
     },
     {
      "quantity": 0.1,
      "log10Quantity": -1.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 22.0
     },
     {
      "quantity": 0.01,
      "log10Quantity": -2.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 19.0
     },
     {
      "quantity": 0.001,
      "log10Quantity": -3.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 16.0
     }
    ],
    "dropped": []
   }
  },
  {
   "name": "e06-undetermined",
   "about": "Level 3 one of three undetermined; level 5 all undetermined, dropped and listed",
   "convention": "quantity",
   "rows": [
    {
     "assay": "TBP",
     "quantity": "1",
     "technical": "1",
     "cq": 15.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "1",
     "technical": "2",
     "cq": 15.1,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "1",
     "technical": "3",
     "cq": 14.9,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.1",
     "technical": "1",
     "cq": 18.4,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.1",
     "technical": "2",
     "cq": 18.3,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.1",
     "technical": "3",
     "cq": 18.5,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.01",
     "technical": "1",
     "cq": 21.7,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.01",
     "technical": "2",
     "cq": null,
     "status": "undetermined",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.01",
     "technical": "3",
     "cq": 21.8,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.001",
     "technical": "1",
     "cq": 25.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.001",
     "technical": "2",
     "cq": 25.2,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.001",
     "technical": "3",
     "cq": 24.9,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.0001",
     "technical": "1",
     "cq": null,
     "status": "undetermined",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.0001",
     "technical": "2",
     "cq": null,
     "status": "undetermined",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.0001",
     "technical": "3",
     "cq": null,
     "status": "undetermined",
     "excluded": false
    }
   ],
   "expected": {
    "status": "fitted",
    "levels": [
     {
      "quantity": 1.0,
      "log10Quantity": 0.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 15.0,
      "residual": -0.02833333333333338
     },
     {
      "quantity": 0.1,
      "log10Quantity": -1.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 18.4,
      "residual": 0.02666666666666657
     },
     {
      "quantity": 0.01,
      "log10Quantity": -2.0,
      "kept": 2,
      "undetermined": 1,
      "meanCq": 21.75,
      "residual": 0.031666666666666995
     },
     {
      "quantity": 0.001,
      "log10Quantity": -3.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 25.03333333333333,
      "residual": -0.03000000000000019
     },
     {
      "quantity": 0.0001,
      "log10Quantity": -4.0,
      "kept": 0,
      "undetermined": 3,
      "meanCq": null
     }
    ],
    "dropped": [
     0.0001
    ],
    "slope": -3.3449999999999998,
    "intercept": 15.028333333333334,
    "rSquared": 0.9999389319799071,
    "amplification": 1.9904609519062118,
    "efficiencyPercent": 99.04609519062119,
    "aboveDoubling": false,
    "carryable": true,
    "carriedValue": 1.9904609519062118,
    "cqRange": [
     15.0,
     25.03333333333333
    ],
    "interval": {
     "slopeLow": -3.4245312119551623,
     "slopeHigh": -3.2654687880448376,
     "eLow": 1.9588932563340344,
     "eHigh": 2.0241129549646883,
     "df": 2
    }
   }
  },
  {
   "name": "e06b-undetermined-two",
   "about": "Two levels left after the undetermined ones are dropped: refused",
   "convention": "quantity",
   "rows": [
    {
     "assay": "TBP",
     "quantity": "1",
     "technical": "1",
     "cq": 15.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "1",
     "technical": "2",
     "cq": 15.1,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "1",
     "technical": "3",
     "cq": 14.9,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.1",
     "technical": "1",
     "cq": 18.4,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.1",
     "technical": "2",
     "cq": 18.3,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.1",
     "technical": "3",
     "cq": 18.5,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.01",
     "technical": "1",
     "cq": null,
     "status": "undetermined",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.01",
     "technical": "2",
     "cq": null,
     "status": "undetermined",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.01",
     "technical": "3",
     "cq": null,
     "status": "undetermined",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.001",
     "technical": "1",
     "cq": null,
     "status": "undetermined",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.001",
     "technical": "2",
     "cq": null,
     "status": "undetermined",
     "excluded": false
    },
    {
     "assay": "TBP",
     "quantity": "0.001",
     "technical": "3",
     "cq": null,
     "status": "undetermined",
     "excluded": false
    }
   ],
   "expected": {
    "status": "refused",
    "reason": "too-few-levels",
    "levels": [
     {
      "quantity": 1.0,
      "log10Quantity": 0.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 15.0
     },
     {
      "quantity": 0.1,
      "log10Quantity": -1.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 18.4
     },
     {
      "quantity": 0.01,
      "log10Quantity": -2.0,
      "kept": 0,
      "undetermined": 3,
      "meanCq": null
     },
     {
      "quantity": 0.001,
      "log10Quantity": -3.0,
      "kept": 0,
      "undetermined": 3,
      "meanCq": null
     }
    ],
    "dropped": [
     0.01,
     0.001
    ]
   }
  },
  {
   "name": "e07-above-doubling",
   "about": "Slope -3.0: E = 10^(1/3), flagged, not carryable",
   "convention": "quantity",
   "rows": [
    {
     "assay": "RPL13A",
     "quantity": "1",
     "technical": "1",
     "cq": 16.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "RPL13A",
     "quantity": "1",
     "technical": "2",
     "cq": 16.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "RPL13A",
     "quantity": "1",
     "technical": "3",
     "cq": 16.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "RPL13A",
     "quantity": "0.1",
     "technical": "1",
     "cq": 19.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "RPL13A",
     "quantity": "0.1",
     "technical": "2",
     "cq": 19.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "RPL13A",
     "quantity": "0.1",
     "technical": "3",
     "cq": 19.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "RPL13A",
     "quantity": "0.01",
     "technical": "1",
     "cq": 22.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "RPL13A",
     "quantity": "0.01",
     "technical": "2",
     "cq": 22.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "RPL13A",
     "quantity": "0.01",
     "technical": "3",
     "cq": 22.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "RPL13A",
     "quantity": "0.001",
     "technical": "1",
     "cq": 25.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "RPL13A",
     "quantity": "0.001",
     "technical": "2",
     "cq": 25.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "RPL13A",
     "quantity": "0.001",
     "technical": "3",
     "cq": 25.0,
     "status": "measured",
     "excluded": false
    }
   ],
   "expected": {
    "status": "fitted",
    "levels": [
     {
      "quantity": 1.0,
      "log10Quantity": 0.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 16.0,
      "residual": 0.0
     },
     {
      "quantity": 0.1,
      "log10Quantity": -1.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 19.0,
      "residual": 0.0
     },
     {
      "quantity": 0.01,
      "log10Quantity": -2.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 22.0,
      "residual": 0.0
     },
     {
      "quantity": 0.001,
      "log10Quantity": -3.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 25.0,
      "residual": 0.0
     }
    ],
    "dropped": [],
    "slope": -3.0,
    "intercept": 16.0,
    "rSquared": 1.0,
    "amplification": 2.154434690031884,
    "efficiencyPercent": 115.44346900318837,
    "aboveDoubling": true,
    "carryable": false,
    "carriedValue": null,
    "cqRange": [
     16.0,
     25.0
    ],
    "interval": {
     "slopeLow": -3.0,
     "slopeHigh": -3.0,
     "eLow": 2.154434690031884,
     "eHigh": 2.154434690031884,
     "df": 2
    }
   }
  },
  {
   "name": "e08a-quantities",
   "about": "Quantities 1, 0.1, 0.01, 0.001",
   "convention": "quantity",
   "rows": [
    {
     "assay": "SDHA",
     "quantity": "1",
     "technical": "1",
     "cq": 15.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "1",
     "technical": "2",
     "cq": 15.2,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "1",
     "technical": "3",
     "cq": 14.9,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.1",
     "technical": "1",
     "cq": 18.5,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.1",
     "technical": "2",
     "cq": 18.4,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.1",
     "technical": "3",
     "cq": 18.6,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.01",
     "technical": "1",
     "cq": 21.9,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.01",
     "technical": "2",
     "cq": 22.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.01",
     "technical": "3",
     "cq": 21.8,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.001",
     "technical": "1",
     "cq": 25.3,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.001",
     "technical": "2",
     "cq": 25.4,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.001",
     "technical": "3",
     "cq": 25.2,
     "status": "measured",
     "excluded": false
    }
   ],
   "expected": {
    "status": "fitted",
    "levels": [
     {
      "quantity": 1.0,
      "log10Quantity": 0.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 15.033333333333333,
      "residual": -0.020000000000000108
     },
     {
      "quantity": 0.1,
      "log10Quantity": -1.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 18.5,
      "residual": 0.026666666666666807
     },
     {
      "quantity": 0.01,
      "log10Quantity": -2.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 21.9,
      "residual": 0.006666666666666702
     },
     {
      "quantity": 0.001,
      "log10Quantity": -3.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 25.3,
      "residual": -0.013333333333333404
     }
    ],
    "dropped": [],
    "slope": -3.42,
    "intercept": 15.053333333333333,
    "rSquared": 0.9999772014819037,
    "amplification": 1.960639106874464,
    "efficiencyPercent": 96.06391068744641,
    "aboveDoubling": false,
    "carryable": true,
    "carriedValue": 1.960639106874464,
    "cqRange": [
     15.033333333333333,
     25.3
    ],
    "interval": {
     "slopeLow": -3.469682754234391,
     "slopeHigh": -3.3703172457656088,
     "eLow": 1.941828128468363,
     "eHigh": 1.980195063402743,
     "df": 2
    }
   }
  },
  {
   "name": "e08b-fold-dilutions",
   "about": "The same series as fold dilutions 1, 10, 100, 1000: the same fit",
   "convention": "fold-dilution",
   "rows": [
    {
     "assay": "SDHA",
     "quantity": "1",
     "technical": "1",
     "cq": 15.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "1",
     "technical": "2",
     "cq": 15.2,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "1",
     "technical": "3",
     "cq": 14.9,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "10",
     "technical": "1",
     "cq": 18.5,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "10",
     "technical": "2",
     "cq": 18.4,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "10",
     "technical": "3",
     "cq": 18.6,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "100",
     "technical": "1",
     "cq": 21.9,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "100",
     "technical": "2",
     "cq": 22.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "100",
     "technical": "3",
     "cq": 21.8,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "1000",
     "technical": "1",
     "cq": 25.3,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "1000",
     "technical": "2",
     "cq": 25.4,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "1000",
     "technical": "3",
     "cq": 25.2,
     "status": "measured",
     "excluded": false
    }
   ],
   "expected": {
    "status": "fitted",
    "levels": [
     {
      "quantity": 1.0,
      "log10Quantity": 0.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 15.033333333333333,
      "residual": -0.020000000000000108
     },
     {
      "quantity": 0.1,
      "log10Quantity": -1.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 18.5,
      "residual": 0.026666666666666807
     },
     {
      "quantity": 0.01,
      "log10Quantity": -2.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 21.9,
      "residual": 0.006666666666666702
     },
     {
      "quantity": 0.001,
      "log10Quantity": -3.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 25.3,
      "residual": -0.013333333333333404
     }
    ],
    "dropped": [],
    "slope": -3.42,
    "intercept": 15.053333333333333,
    "rSquared": 0.9999772014819037,
    "amplification": 1.960639106874464,
    "efficiencyPercent": 96.06391068744641,
    "aboveDoubling": false,
    "carryable": true,
    "carriedValue": 1.960639106874464,
    "cqRange": [
     15.033333333333333,
     25.3
    ],
    "interval": {
     "slopeLow": -3.469682754234391,
     "slopeHigh": -3.3703172457656088,
     "eLow": 1.941828128468363,
     "eHigh": 1.980195063402743,
     "df": 2
    }
   }
  },
  {
   "name": "e08c-excluded-well",
   "about": "An excluded outlier (30.0 at level 2) never enters the level mean",
   "convention": "quantity",
   "rows": [
    {
     "assay": "SDHA",
     "quantity": "1",
     "technical": "1",
     "cq": 15.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "1",
     "technical": "2",
     "cq": 15.2,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "1",
     "technical": "3",
     "cq": 14.9,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.1",
     "technical": "1",
     "cq": 18.5,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.1",
     "technical": "2",
     "cq": 18.4,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.1",
     "technical": "3",
     "cq": 30.0,
     "status": "measured",
     "excluded": true
    },
    {
     "assay": "SDHA",
     "quantity": "0.01",
     "technical": "1",
     "cq": 21.9,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.01",
     "technical": "2",
     "cq": 22.0,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.01",
     "technical": "3",
     "cq": 21.8,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.001",
     "technical": "1",
     "cq": 25.3,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.001",
     "technical": "2",
     "cq": 25.4,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.001",
     "technical": "3",
     "cq": 25.2,
     "status": "measured",
     "excluded": false
    }
   ],
   "expected": {
    "status": "fitted",
    "levels": [
     {
      "quantity": 1.0,
      "log10Quantity": 0.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 15.033333333333333,
      "residual": 1.7763568394002506e-16
     },
     {
      "quantity": 0.1,
      "log10Quantity": -1.0,
      "kept": 2,
      "undetermined": 0,
      "meanCq": 18.45,
      "residual": -0.008333333333333689
     },
     {
      "quantity": 0.01,
      "log10Quantity": -2.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 21.9,
      "residual": 0.016666666666666843
     },
     {
      "quantity": 0.001,
      "log10Quantity": -3.0,
      "kept": 3,
      "undetermined": 0,
      "meanCq": 25.3,
      "residual": -0.008333333333333333
     }
    ],
    "dropped": [],
    "slope": -3.425,
    "intercept": 15.033333333333333,
    "rSquared": 0.9999928961379854,
    "amplification": 1.9587129872305569,
    "efficiencyPercent": 95.87129872305569,
    "aboveDoubling": false,
    "carryable": true,
    "carriedValue": 1.9587129872305569,
    "cqRange": [
     15.033333333333333,
     25.3
    ],
    "interval": {
     "slopeLow": -3.4527735039443788,
     "slopeHigh": -3.3972264960556213,
     "eLow": 1.9481493191185781,
     "eHigh": 1.969508073452442,
     "df": 2
    }
   }
  },
  {
   "name": "e09-bad-quantity",
   "about": "A quantity of 0: refused",
   "convention": "quantity",
   "rows": [
    {
     "assay": "SDHA",
     "quantity": "1",
     "technical": "1",
     "cq": 15,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "1",
     "technical": "2",
     "cq": 15,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "1",
     "technical": "3",
     "cq": 15,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0",
     "technical": "1",
     "cq": 18,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0",
     "technical": "2",
     "cq": 18,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0",
     "technical": "3",
     "cq": 18,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.01",
     "technical": "1",
     "cq": 21,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.01",
     "technical": "2",
     "cq": 21,
     "status": "measured",
     "excluded": false
    },
    {
     "assay": "SDHA",
     "quantity": "0.01",
     "technical": "3",
     "cq": 21,
     "status": "measured",
     "excluded": false
    }
   ],
   "expected": {
    "status": "refused",
    "reason": "bad-quantity"
   }
  }
 ],
 "genorm": [
  {
   "name": "g10-hand",
   "about": "E = 2: V_AB = 0, V_AC = V_BC = sqrt(5/3); M_A = M_B (tied), M_C = sqrt(5/3)",
   "table": {
    "S1": {
     "A": 20,
     "B": 25,
     "C": 18
    },
    "S2": {
     "A": 21,
     "B": 26,
     "C": 20
    },
    "S3": {
     "A": 22,
     "B": 27,
     "C": 19
    },
    "S4": {
     "A": 23,
     "B": 28,
     "C": 23
    }
   },
   "expected": {
    "status": "ranked",
    "ranking": [
     {
      "assay": "A",
      "m": 0.6454972243679028
     },
     {
      "assay": "B",
      "m": 0.6454972243679028
     },
     {
      "assay": "C",
      "m": 1.2909944487358056
     }
    ],
    "samples": 4,
    "dropped": []
   }
  },
  {
   "name": "g11-two-genes",
   "about": "C removed: no ranking, the pairwise SD 0",
   "table": {
    "S1": {
     "A": 20,
     "B": 25
    },
    "S2": {
     "A": 21,
     "B": 26
    },
    "S3": {
     "A": 22,
     "B": 27
    },
    "S4": {
     "A": 23,
     "B": 28
    }
   },
   "expected": {
    "status": "pair",
    "assays": [
     "A",
     "B"
    ],
    "sd": 0.0,
    "samples": 4,
    "dropped": []
   }
  },
  {
   "name": "g12-incomplete",
   "about": "A fifth sample with C undetermined: dropped and listed, M as g10",
   "table": {
    "S1": {
     "A": 20,
     "B": 25,
     "C": 18
    },
    "S2": {
     "A": 21,
     "B": 26,
     "C": 20
    },
    "S3": {
     "A": 22,
     "B": 27,
     "C": 19
    },
    "S4": {
     "A": 23,
     "B": 28,
     "C": 23
    },
    "S5": {
     "A": 21,
     "B": 26,
     "C": null
    }
   },
   "expected": {
    "status": "ranked",
    "ranking": [
     {
      "assay": "A",
      "m": 0.6454972243679028
     },
     {
      "assay": "B",
      "m": 0.6454972243679028
     },
     {
      "assay": "C",
      "m": 1.2909944487358056
     }
    ],
    "samples": 4,
    "dropped": [
     "S5"
    ]
   }
  },
  {
   "name": "g13-efficiency",
   "about": "g10 with E_C = 1.9 under the efficiency-corrected method",
   "table": {
    "S1": {
     "A": 20,
     "B": 25,
     "C": 18
    },
    "S2": {
     "A": 21,
     "B": 26,
     "C": 20
    },
    "S3": {
     "A": 22,
     "B": 27,
     "C": 19
    },
    "S4": {
     "A": 23,
     "B": 28,
     "C": 23
    }
   },
   "efficiencies": {
    "C": 1.9
   },
   "expected": {
    "status": "ranked",
    "ranking": [
     {
      "assay": "A",
      "m": 0.580277021813961
     },
     {
      "assay": "B",
      "m": 0.580277021813961
     },
     {
      "assay": "C",
      "m": 1.160554043627922
     }
    ],
    "samples": 4,
    "dropped": []
   }
  },
  {
   "name": "g14-two-samples",
   "about": "Two complete samples: M withheld",
   "table": {
    "S1": {
     "A": 20,
     "B": 25,
     "C": 18
    },
    "S2": {
     "A": 21,
     "B": 26,
     "C": 20
    }
   },
   "expected": {
    "status": "withheld",
    "reason": "too-few-samples",
    "samples": 2,
    "dropped": []
   }
  }
 ]
}