{
 "about": {
  "method": "qpcr-fold-change-welch-interval",
  "origin": "Original synthetic Cq tables, not experimental data",
  "ruling": "CSO memo of 11 October 2026, item 9 (docs/board/memos/2026-10-11-cso-assay-depth-stage.md); roadmap A6",
  "model": "difference of mean normalised log2 quantities, treated minus the run's calibrator samples, with a two-sample Welch t-interval (Welch-Satterthwaite df), 95 percent",
  "minimumBiologicalSamples": 3,
  "withheldReasons": [
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   "calibrator-unresolved",
   "calibrator-n",
   "treated-n",
   "no-scatter"
  ],
  "tolerances": {
   "normalised log2 quantities, differences, standard errors and bounds": "1e-9 absolute (log2 units)",
   "degrees of freedom and t quantile": "1e-9 relative",
   "fold bounds": "1e-9 relative",
   "n, statuses and reasons": "exact"
  },
  "recordedOn": "2026-10-12",
  "script": "pipeline/assay-analyser/oracles/qpcr_welch.py",
  "scriptSha256": "38759b153ef3d2709b0a93274881f9b78799e66f308d15717e8be3ef772f87d2",
  "helper": {
   "script": "pipeline/assay-analyser/oracles/stage_a_oracle.py",
   "sha256": "492d85ca2fa6750db80b1c64214fd4a0b13cd4c588267244f6262c504c73e3e8"
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  "environment": {
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   "r": "R version 4.4.3 (2025-02-28)",
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   "python": "3.11.15",
   "numpy": "2.0.2",
   "scipy": "1.13.1",
   "recordedOn": "2026-10-12",
   "cpu": "AMD EPYC 7763 64-Core Processor",
   "cpuClass": "x86-64-v3",
   "simd": [
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    "SSE41",
    "POPCNT",
    "SSE42",
    "AVX",
    "F16C",
    "FMA3",
    "AVX2"
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   "openblasCore": "Haswell",
   "threads": 1
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  "crossCheck": {
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   "ran": true,
   "settings": "t.test(treated, calibrator, var.equal = FALSE, conf.level = 0.95) on the per-sample normalised log2 quantities",
   "tolerances": {
    "bounds": "1e-9 absolute",
    "df": "1e-9 relative"
   },
   "cases": 8,
   "agreeing": 8,
   "result": [
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   ],
   "scipy": {
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    "agreeing": 8,
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    {
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    {
     "case": "two-references",
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    {
     "case": "treated-two-samples",
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     "reason": "treated-n"
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    {
     "case": "treated-two-samples",
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     "reason": "calibrator-group"
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    {
     "case": "calibrator-two-samples",
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    {
     "case": "calibrator-two-samples",
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     "reason": "calibrator-group"
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    {
     "case": "no-scatter",
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     "reason": "no-scatter"
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    {
     "case": "no-scatter",
     "run": "R1",
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    {
     "case": "calibrator-flat",
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    {
     "case": "two-runs",
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    {
     "case": "two-runs",
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    {
     "case": "two-runs",
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    {
     "case": "unresolved-sample",
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   ]
  }
 },
 "oracle": {
  "engine": "numpy and scipy.stats.t.ppf",
  "method": "the hand Welch formula on per-sample normalised log2 quantities computed here from the Cq table"
 },
 "cases": [
  {
   "name": "ddcq-basic",
   "method": "delta-delta-cq",
   "targetAssays": [
    "IL6"
   ],
   "referenceAssays": [
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   ],
   "efficiencies": {},
   "readings": [
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     "run": "R1",
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    {
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    {
     "run": "R1",
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    {
     "run": "R1",
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    {
     "run": "R1",
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    {
     "run": "R1",
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     "condition": "vehicle",
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     "assay": "IL6",
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    },
    {
     "run": "R1",
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     "assay": "IL6",
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    {
     "run": "R1",
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    {
     "run": "R1",
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     "assay": "ACTB",
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    {
     "run": "R1",
     "sample": "D1",
     "condition": "drug",
     "calibrator": false,
     "assay": "IL6",
     "role": "target",
     "technical": "t1",
     "cq": 25.27
    },
    {
     "run": "R1",
     "sample": "D1",
     "condition": "drug",
     "calibrator": false,
     "assay": "IL6",
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     "technical": "t2",
     "cq": 25.36
    },
    {
     "run": "R1",
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     "condition": "drug",
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     "assay": "ACTB",
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     "cq": 18.130000000000003
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    {
     "run": "R1",
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     "cq": 18.080000000000002
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    {
     "run": "R1",
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     "assay": "IL6",
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    {
     "run": "R1",
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     "assay": "IL6",
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     "cq": 25.07
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    {
     "run": "R1",
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     "assay": "ACTB",
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     "cq": 17.92
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    {
     "run": "R1",
     "sample": "D2",
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     "assay": "ACTB",
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     "cq": 17.87
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    {
     "run": "R1",
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     "assay": "IL6",
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    {
     "run": "R1",
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     "assay": "IL6",
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     "cq": 25.71
    },
    {
     "run": "R1",
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     "assay": "ACTB",
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   ],
   "expected": {
    "normalised": [
     {
      "run": "R1",
      "sample": "D1",
      "normalisedLog2Quantity": -7.209999999999994
     },
     {
      "run": "R1",
      "sample": "D2",
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     },
     {
      "run": "R1",
      "sample": "D3",
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     },
     {
      "run": "R1",
      "sample": "V1",
      "normalisedLog2Quantity": -9.080000000000005
     },
     {
      "run": "R1",
      "sample": "V2",
      "normalisedLog2Quantity": -9.239999999999995
     },
     {
      "run": "R1",
      "sample": "V3",
      "normalisedLog2Quantity": -8.93
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    ],
    "groups": [
     {
      "run": "R1",
      "condition": "drug",
      "target": "IL6",
      "samples": [
       "D1",
       "D2",
       "D3"
      ],
      "nTreated": 3,
      "nCalibrator": 3,
      "interval": {
       "status": "calculated",
       "level": 0.95,
       "differenceLog2": 1.850000000000004,
       "se": 0.11205157542647706,
       "df": 3.7166616699800676,
       "t": 2.861945780404081,
       "lowerLog2": 1.5293144665205685,
       "upperLog2": 2.17068553347944,
       "foldChange": 3.605001850443331,
       "lowerFold": 2.8864864771816054,
       "upperFold": 4.502372848248819,
       "treatedSdLog2": 0.11676186592091563,
       "calibratorSdLog2": 0.1550268793897773
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      "vectors": {
       "treated": [
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        -7.1299999999999955,
        -7.359999999999999
       ],
       "calibrator": [
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        -9.239999999999995,
        -8.93
       ]
      }
     },
     {
      "run": "R1",
      "condition": "vehicle",
      "target": "IL6",
      "samples": [
       "V1",
       "V2",
       "V3"
      ],
      "nTreated": 3,
      "nCalibrator": 3,
      "interval": {
       "status": "withheld",
       "reason": "calibrator-group"
      }
     }
    ]
   }
  },
  {
   "name": "efficiency-corrected",
   "method": "efficiency-corrected",
   "targetAssays": [
    "IL6"
   ],
   "referenceAssays": [
    "ACTB"
   ],
   "efficiencies": {
    "IL6": 1.92,
    "ACTB": 1.97
   },
   "readings": [
    {
     "run": "R1",
     "sample": "V1",
     "condition": "vehicle",
     "calibrator": true,
     "assay": "IL6",
     "role": "target",
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     "cq": 27.060000000000002
    },
    {
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    {
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    {
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     "cq": 18.0
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    {
     "run": "R1",
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     "calibrator": true,
     "assay": "IL6",
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     "technical": "t1",
     "cq": 27.41
    },
    {
     "run": "R1",
     "sample": "V2",
     "condition": "vehicle",
     "calibrator": true,
     "assay": "IL6",
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     "technical": "t2",
     "cq": 27.5
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       "calibrator": [
        -9.080000000000005,
        -9.239999999999995,
        -8.93
       ]
      }
     },
     {
      "run": "R1",
      "condition": "vehicle",
      "target": "IL6",
      "samples": [
       "V1",
       "V2",
       "V3"
      ],
      "nTreated": 3,
      "nCalibrator": 3,
      "interval": {
       "status": "withheld",
       "reason": "calibrator-group"
      }
     }
    ]
   }
  }
 ]
}