{ "about": { "method": "combination-hsa-observed@1.0.0; combination-bliss-observed@1.0.0", "recordedOn": "2026-10-18", "script": "pipeline/assay-analyser/oracles/combination_hsa_bliss_3.py", "scriptSha256": "ba3629f091b93942390c7fdc2a2a875c8570e0cf3158f5c321225601eefdca7b", "source": "docs/design/product-expansion/13-combination-analysis.md; docs/board/memos/2026-10-17-cso-gemini-rebuild-questions.md; docs/board/memos/2026-10-17-cto-gemini-rebuild-questions.md", "tolerances": { "expectedFraction": 1e-09, "excessPercentagePoints": 1e-09, "vehicleMean": 1e-09, "counts": "exact", "status": "exact", "reason": "exact", "contributingIds": "exact" }, "environment": { "image": "local", "python": "3.9.6", "platform": "macOS-27.2-arm64-arm-64bit" }, "crossCheck": { "tool": "synergy", "version": "1.0.0", "adapter": "V = 1 \u2212 E; exact-lookup single-agent models; 100 \u00d7 (V_ref \u2212 V_obs)", "ran": false, "reason": "SYNERGY_PYTHON not set; isolated GPL subprocess skipped" } }, "cases": [ { 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null }, "bliss": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null } }, { "doseA": 7.0, "doseB": 1.0, "observedMean": null, "observedMeanFraction": null, "marginA": null, "marginAFraction": null, "marginB": 0.2, "marginBFraction": "1/5", "retainedCount": 0, "excludedCount": 0, "contributingIds": [ "b1" ], "hsa": { "status": "withheld", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": "missing-combination", "qualification": null }, "bliss": { "status": "withheld", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": "missing-combination" } }, { "doseA": 7.0, "doseB": 2.0, "observedMean": null, "observedMeanFraction": null, "marginA": null, "marginAFraction": null, "marginB": null, "marginBFraction": null, "retainedCount": 0, "excludedCount": 0, "contributingIds": [], "hsa": { "status": "withheld", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": "missing-combination", "qualification": null }, "bliss": { "status": "withheld", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": "missing-combination" } }, { "doseA": 7.0, "doseB": 3.0, "observedMean": null, "observedMeanFraction": null, "marginA": null, "marginAFraction": null, "marginB": 0.3, "marginBFraction": "3/10", "retainedCount": 0, "excludedCount": 0, "contributingIds": [ "b3" ], "hsa": { "status": "withheld", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": "missing-combination", "qualification": null }, "bliss": { "status": "withheld", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": "missing-combination" } }, { "doseA": 7.0, "doseB": 4.0, "observedMean": null, "observedMeanFraction": null, "marginA": null, "marginAFraction": null, "marginB": 0.4, "marginBFraction": "2/5", "retainedCount": 0, "excludedCount": 0, "contributingIds": [ "b4" ], "hsa": { "status": "withheld", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": "missing-combination", "qualification": null }, "bliss": { "status": "withheld", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": "missing-combination" } }, { "doseA": 7.0, "doseB": 5.0, "observedMean": null, "observedMeanFraction": null, "marginA": null, "marginAFraction": null, "marginB": null, "marginBFraction": null, "retainedCount": 0, "excludedCount": 0, "contributingIds": [], "hsa": { "status": "withheld", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": "missing-combination", "qualification": null }, "bliss": { "status": "withheld", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": "missing-combination" } }, { "doseA": 7.0, "doseB": 6.0, "observedMean": null, "observedMeanFraction": null, "marginA": null, "marginAFraction": null, "marginB": null, "marginBFraction": null, "retainedCount": 0, "excludedCount": 0, "contributingIds": [], "hsa": { "status": "withheld", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": "missing-combination", "qualification": null }, "bliss": { "status": "withheld", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": "missing-combination" } }, { "doseA": 7.0, "doseB": 7.0, "observedMean": null, "observedMeanFraction": null, "marginA": null, "marginAFraction": null, "marginB": null, "marginBFraction": null, "retainedCount": 0, "excludedCount": 0, "contributingIds": [], "hsa": { "status": "withheld", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": "missing-combination", "qualification": null }, "bliss": { "status": "withheld", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": "missing-combination" } } ] } }, { "name": "vehicle-missing", "description": "No (0,0) observation refuses analysis with missing-vehicle-control", "input": { "mode": "already-normalised", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "a1", "doseA": 1, "doseB": 0, "response": 0.2 }, { "id": "b1", "doseA": 0, "doseB": 1, "response": 0.3 }, { "id": "ab1", "doseA": 1, "doseB": 1, "response": 0.44 } ] }, "expected": { "status": "refused", "refusal": "missing-vehicle-control", "vehicleMean": null, "vehicleMeanFraction": null, "vehicleCount": 0, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [] } }, { "name": "vehicle-nonzero-disclosed", "description": "Non-zero vehicle mean 0.05 is disclosed with fixed qualification and not re-zeroed", "input": { "mode": "already-normalised", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.04 }, { "id": "v2", "doseA": 0, "doseB": 0, "response": 0.05 }, { "id": "v3", "doseA": 0, "doseB": 0, "response": 0.06 }, { "id": "a1", "doseA": 1, "doseB": 0, "response": 0.2 }, { "id": "b1", "doseA": 0, "doseB": 1, "response": 0.3 }, { "id": "ab1", "doseA": 1, "doseB": 1, "response": 0.44 } ] }, "expected": { "status": "calculated", "refusal": null, "vehicleMean": 0.05, "vehicleMeanFraction": "1/20", "vehicleCount": 3, "vehicleQualification": "The declared scale places vehicle at E = 0; the measured vehicle mean is 0.05 (n = 3). Results are not re-zeroed.", "outOfRangeCount": 0, "cells": [ { "doseA": 0.0, "doseB": 0.0, "observedMean": 0.05, "observedMeanFraction": "1/20", "marginA": 0.05, "marginAFraction": "1/20", "marginB": 0.05, "marginBFraction": "1/20", "retainedCount": 3, "excludedCount": 0, "contributingIds": [ "v1", "v2", "v3" ], "hsa": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null, "qualification": null }, "bliss": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null } }, { "doseA": 0.0, "doseB": 1.0, "observedMean": 0.3, "observedMeanFraction": "3/10", "marginA": 0.05, "marginAFraction": "1/20", "marginB": 0.3, "marginBFraction": "3/10", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "b1" ], "hsa": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null, "qualification": null }, "bliss": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null } }, { "doseA": 1.0, "doseB": 0.0, "observedMean": 0.2, "observedMeanFraction": "1/5", "marginA": 0.2, "marginAFraction": "1/5", "marginB": 0.05, "marginBFraction": "1/20", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "a1" ], "hsa": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null, "qualification": null }, "bliss": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null } }, { "doseA": 1.0, "doseB": 1.0, "observedMean": 0.44, "observedMeanFraction": "11/25", "marginA": 0.2, "marginAFraction": "1/5", "marginB": 0.3, "marginBFraction": "3/10", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "a1", "ab1", "b1" ], "hsa": { "status": "calculated", "expectedFraction": 0.3, "expectedFractionStr": "3/10", "excessPercentagePoints": 14.0, "excessPercentagePointsStr": "14", "reason": null, "qualification": null }, "bliss": { "status": "calculated", "expectedFraction": 0.44, "expectedFractionStr": "11/25", "excessPercentagePoints": 0.0, "excessPercentagePointsStr": "0", "reason": null } } ] } }, { "name": "vehicle-zero-unqualified", "description": "Exact zero vehicle mean has no qualification", "input": { "mode": "already-normalised", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "v2", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "a1", "doseA": 1, "doseB": 0, "response": 0.2 }, { "id": "b1", "doseA": 0, "doseB": 1, "response": 0.3 }, { "id": "ab1", "doseA": 1, "doseB": 1, "response": 0.44 } ] }, "expected": { "status": "calculated", "refusal": null, "vehicleMean": 0.0, "vehicleMeanFraction": "0", "vehicleCount": 2, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [ { "doseA": 0.0, "doseB": 0.0, "observedMean": 0.0, "observedMeanFraction": "0", "marginA": 0.0, "marginAFraction": "0", "marginB": 0.0, "marginBFraction": "0", "retainedCount": 2, "excludedCount": 0, "contributingIds": [ "v1", "v2" ], "hsa": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null, "qualification": null }, "bliss": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null } }, { "doseA": 0.0, "doseB": 1.0, "observedMean": 0.3, "observedMeanFraction": "3/10", "marginA": 0.0, "marginAFraction": "0", "marginB": 0.3, "marginBFraction": "3/10", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "b1" ], "hsa": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null, "qualification": null }, "bliss": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null } }, { "doseA": 1.0, "doseB": 0.0, "observedMean": 0.2, "observedMeanFraction": "1/5", "marginA": 0.2, "marginAFraction": "1/5", "marginB": 0.0, "marginBFraction": "0", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "a1" ], "hsa": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null, "qualification": null }, "bliss": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null } }, { "doseA": 1.0, "doseB": 1.0, "observedMean": 0.44, "observedMeanFraction": "11/25", "marginA": 0.2, "marginAFraction": "1/5", "marginB": 0.3, "marginBFraction": "3/10", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "a1", "ab1", "b1" ], "hsa": { "status": "calculated", "expectedFraction": 0.3, "expectedFractionStr": "3/10", "excessPercentagePoints": 14.0, "excessPercentagePointsStr": "14", "reason": null, "qualification": null }, "bliss": { "status": "calculated", "expectedFraction": 0.44, "expectedFractionStr": "11/25", "excessPercentagePoints": 0.0, "excessPercentagePointsStr": "0", "reason": null } } ] } }, { "name": "raw-missing-no-effect", "description": "Raw path with no no-effect controls refuses with missing-no-effect-control", "input": { "mode": "raw-with-controls", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.0 } ], "controls": { "fullEffect": [ 100.0, 100.0 ] } }, "expected": { "status": "refused", "refusal": "missing-no-effect-control", "vehicleMean": null, "vehicleMeanFraction": null, "vehicleCount": 0, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [] } }, { "name": "raw-too-few-no-effect", "description": "Raw path with 1 no-effect control refuses with too-few-no-effect-controls", "input": { "mode": "raw-with-controls", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.0 } ], "controls": { "noEffect": [ 0.0 ], "fullEffect": [ 100.0, 100.0 ] } }, "expected": { "status": "refused", "refusal": "too-few-no-effect-controls", "vehicleMean": null, "vehicleMeanFraction": null, "vehicleCount": 0, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [] } }, { "name": "raw-missing-full-effect", "description": "Raw path with no full-effect controls refuses with missing-full-effect-control", "input": { "mode": "raw-with-controls", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.0 } ], "controls": { "noEffect": [ 0.0, 0.0 ] } }, "expected": { "status": "refused", "refusal": "missing-full-effect-control", "vehicleMean": null, "vehicleMeanFraction": null, "vehicleCount": 0, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [] } }, { "name": "raw-too-few-full-effect", "description": "Raw path with 1 full-effect control refuses with too-few-full-effect-controls", "input": { "mode": "raw-with-controls", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.0 } ], "controls": { "noEffect": [ 0.0, 0.0 ], "fullEffect": [ 100.0 ] } }, "expected": { "status": "refused", "refusal": "too-few-full-effect-controls", "vehicleMean": null, "vehicleMeanFraction": null, "vehicleCount": 0, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [] } }, { "name": "raw-zero-control-span", "description": "Zero span between full and no-effect controls refuses with zero-control-span", "input": { "mode": "raw-with-controls", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 50.0 } ], "controls": { "noEffect": [ 50.0, 50.0 ], "fullEffect": [ 50.0, 50.0 ] } }, "expected": { "status": "refused", "refusal": "zero-control-span", "vehicleMean": null, "vehicleMeanFraction": null, "vehicleCount": 0, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [] } }, { "name": "raw-direction-contradicts", "description": "Remaining response declared but full > no-effect refuses with direction-contradicts-controls", "input": { "mode": "raw-with-controls", "scale": "fraction", "direction": "remaining-response-decreasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.0 } ], "controls": { "noEffect": [ 0.0, 0.0 ], "fullEffect": [ 100.0, 100.0 ] } }, "expected": { "status": "refused", "refusal": "direction-contradicts-controls", "vehicleMean": null, "vehicleMeanFraction": null, "vehicleCount": 0, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [] } }, { "name": "bliss-undeclared", "description": "Bliss declaration unticked: Bliss withheld (bliss-interpretation-undeclared), HSA calculated", "input": { "mode": "already-normalised", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": false, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "a1", "doseA": 1, "doseB": 0, "response": 0.2 }, { "id": "b1", "doseA": 0, "doseB": 1, "response": 0.3 }, { "id": "ab1", "doseA": 1, "doseB": 1, "response": 0.44 } ] }, "expected": { "status": "calculated", "refusal": null, "vehicleMean": 0.0, "vehicleMeanFraction": "0", "vehicleCount": 1, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [ { "doseA": 0.0, "doseB": 0.0, "observedMean": 0.0, "observedMeanFraction": "0", "marginA": 0.0, "marginAFraction": "0", "marginB": 0.0, "marginBFraction": "0", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "v1" ], "hsa": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null, "qualification": null }, "bliss": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null } }, { "doseA": 0.0, "doseB": 1.0, "observedMean": 0.3, "observedMeanFraction": "3/10", "marginA": 0.0, "marginAFraction": "0", "marginB": 0.3, "marginBFraction": "3/10", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "b1" ], "hsa": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null, "qualification": null }, "bliss": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null } }, { "doseA": 1.0, "doseB": 0.0, "observedMean": 0.2, "observedMeanFraction": "1/5", "marginA": 0.2, "marginAFraction": "1/5", "marginB": 0.0, "marginBFraction": "0", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "a1" ], "hsa": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null, "qualification": null }, "bliss": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null } }, { "doseA": 1.0, "doseB": 1.0, "observedMean": 0.44, "observedMeanFraction": "11/25", "marginA": 0.2, "marginAFraction": "1/5", "marginB": 0.3, "marginBFraction": "3/10", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "a1", "ab1", "b1" ], "hsa": { "status": "calculated", "expectedFraction": 0.3, "expectedFractionStr": "3/10", "excessPercentagePoints": 14.0, "excessPercentagePointsStr": "14", "reason": null, "qualification": null }, "bliss": { "status": "withheld", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": "bliss-interpretation-undeclared" } } ] } }, { "name": "multiple-bio-replicates", "description": "Multiple biological replicate IDs refuse analysis with multiple-biological-replicates", "input": { "mode": "already-normalised", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.0, "biologicalReplicateId": "bio-1" }, { "id": "a1", "doseA": 1, "doseB": 0, "response": 0.2, "biologicalReplicateId": "bio-2" }, { "id": "b1", "doseA": 0, "doseB": 1, "response": 0.3 }, { "id": "ab1", "doseA": 1, "doseB": 1, "response": 0.44 } ] }, "expected": { "status": "refused", "refusal": "multiple-biological-replicates", "vehicleMean": null, "vehicleMeanFraction": null, "vehicleCount": 0, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [] } }, { "name": "near-equal-doses", "description": "Near-equal doses 1.0 and 1.0000001 remain distinct levels", "input": { "mode": "already-normalised", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1.0, 1.0000001 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "a1", "doseA": 1.0, "doseB": 0, "response": 0.2 }, { "id": "a2", "doseA": 1.0000001, "doseB": 0, "response": 0.25 }, { "id": "b1", "doseA": 0, "doseB": 1, "response": 0.3 }, { "id": "ab1", "doseA": 1.0, "doseB": 1, "response": 0.44 }, { "id": "ab2", "doseA": 1.0000001, "doseB": 1, "response": 0.48 } ] }, "expected": { "status": "calculated", "refusal": null, "vehicleMean": 0.0, "vehicleMeanFraction": "0", "vehicleCount": 1, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [ { "doseA": 0.0, "doseB": 0.0, "observedMean": 0.0, "observedMeanFraction": "0", "marginA": 0.0, "marginAFraction": "0", "marginB": 0.0, "marginBFraction": "0", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "v1" ], "hsa": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null, "qualification": null }, "bliss": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null } }, { "doseA": 0.0, "doseB": 1.0, "observedMean": 0.3, "observedMeanFraction": "3/10", "marginA": 0.0, "marginAFraction": "0", "marginB": 0.3, "marginBFraction": "3/10", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "b1" ], "hsa": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null, "qualification": null }, "bliss": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null } }, { "doseA": 1.0, "doseB": 0.0, "observedMean": 0.2, "observedMeanFraction": "1/5", "marginA": 0.2, "marginAFraction": "1/5", "marginB": 0.0, "marginBFraction": "0", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "a1" ], "hsa": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null, "qualification": null }, "bliss": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null } }, { "doseA": 1.0, "doseB": 1.0, "observedMean": 0.44, "observedMeanFraction": "11/25", "marginA": 0.2, "marginAFraction": "1/5", "marginB": 0.3, "marginBFraction": "3/10", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "a1", "ab1", "b1" ], "hsa": { "status": "calculated", "expectedFraction": 0.3, "expectedFractionStr": "3/10", "excessPercentagePoints": 14.0, "excessPercentagePointsStr": "14", "reason": null, "qualification": null }, "bliss": { "status": "calculated", "expectedFraction": 0.44, "expectedFractionStr": "11/25", "excessPercentagePoints": 0.0, "excessPercentagePointsStr": "0", "reason": null } }, { "doseA": 1.0000001, "doseB": 0.0, "observedMean": 0.25, "observedMeanFraction": "1/4", "marginA": 0.25, "marginAFraction": "1/4", "marginB": 0.0, "marginBFraction": "0", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "a2" ], "hsa": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null, "qualification": null }, "bliss": { "status": "not-applicable", "expectedFraction": null, "expectedFractionStr": null, "excessPercentagePoints": null, "excessPercentagePointsStr": null, "reason": null } }, { "doseA": 1.0000001, "doseB": 1.0, "observedMean": 0.48, "observedMeanFraction": "12/25", "marginA": 0.25, "marginAFraction": "1/4", "marginB": 0.3, "marginBFraction": "3/10", "retainedCount": 1, "excludedCount": 0, "contributingIds": [ "a2", "ab2", "b1" ], "hsa": { "status": "calculated", "expectedFraction": 0.3, "expectedFractionStr": "3/10", "excessPercentagePoints": 18.0, "excessPercentagePointsStr": "18", "reason": null, "qualification": null }, "bliss": { "status": "calculated", "expectedFraction": 0.475, "expectedFractionStr": "19/40", "excessPercentagePoints": 0.5, "excessPercentagePointsStr": "1/2", "reason": null } } ] } }, { "name": "refusal-non-finite-response", "description": "Non-finite response refused at import with non-finite-response", "input": { "mode": "already-normalised", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "a1", "doseA": 1, "doseB": 0, "response": null }, { "id": "b1", "doseA": 0, "doseB": 1, "response": 0.3 }, { "id": "ab1", "doseA": 1, "doseB": 1, "response": 0.44 } ] }, "expected": { "status": "refused", "refusal": "non-finite-response", "vehicleMean": null, "vehicleMeanFraction": null, "vehicleCount": 0, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [] } }, { "name": "refusal-negative-dose", "description": "Negative dose refused with negative-dose", "input": { "mode": "already-normalised", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "bad1", "doseA": -1.0, "doseB": 0, "response": 0.2 }, { "id": "b1", "doseA": 0, "doseB": 1, "response": 0.3 }, { "id": "ab1", "doseA": 1, "doseB": 1, "response": 0.44 } ] }, "expected": { "status": "refused", "refusal": "negative-dose", "vehicleMean": null, "vehicleMeanFraction": null, "vehicleCount": 0, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [] } }, { "name": "refusal-nan-dose", "description": "NaN dose refused with nan-dose", "input": { "mode": "already-normalised", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "bad1", "doseA": null, "doseB": 0, "response": 0.2 }, { "id": "b1", "doseA": 0, "doseB": 1, "response": 0.3 }, { "id": "ab1", "doseA": 1, "doseB": 1, "response": 0.44 } ] }, "expected": { "status": "refused", "refusal": "nan-dose", "vehicleMean": null, "vehicleMeanFraction": null, "vehicleCount": 0, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [] } }, { "name": "refusal-underflow-dose", "description": "Underflow dose refused with underflow-dose", "input": { "mode": "already-normalised", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1e-320 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "bad1", "doseA": 1e-320, "doseB": 0, "response": 0.2 }, { "id": "b1", "doseA": 0, "doseB": 1, "response": 0.3 }, { "id": "ab1", "doseA": 1e-320, "doseB": 1, "response": 0.44 } ] }, "expected": { "status": "refused", "refusal": "underflow-dose", "vehicleMean": null, "vehicleMeanFraction": null, "vehicleCount": 0, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [] } }, { "name": "refusal-duplicate-axis-level", "description": "Duplicate axis level refused with duplicate-axis-level", "input": { "mode": "already-normalised", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1.0, 1.0 ], "dosesB": [ 0, 1 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "a1", "doseA": 1.0, "doseB": 0, "response": 0.2 }, { "id": "b1", "doseA": 0, "doseB": 1, "response": 0.3 }, { "id": "ab1", "doseA": 1.0, "doseB": 1, "response": 0.44 } ] }, "expected": { "status": "refused", "refusal": "duplicate-axis-level", "vehicleMean": null, "vehicleMeanFraction": null, "vehicleCount": 0, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [] } }, { "name": "refusal-off-axis-observation", "description": "Observation at dose not on axis refused with off-axis-observation", "input": { "mode": "already-normalised", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1.0, 2.0 ], "dosesB": [ 0, 1.0 ], "observations": [ { "id": "v1", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "a1", "doseA": 1.0, "doseB": 0, "response": 0.2 }, { "id": "bad1", "doseA": 1.5, "doseB": 0, "response": 0.25 }, { "id": "b1", "doseA": 0, "doseB": 1.0, "response": 0.3 }, { "id": "ab1", "doseA": 1.0, "doseB": 1.0, "response": 0.44 } ] }, "expected": { "status": "refused", "refusal": "off-axis-observation", "vehicleMean": null, "vehicleMeanFraction": null, "vehicleCount": 0, "vehicleQualification": null, "outOfRangeCount": 0, "cells": [] } }, { "name": "max-rows-4096", "description": "Maximum 4,096 observations on 8x8 matrix are accepted and calculated", "input": { "mode": "already-normalised", "scale": "fraction", "direction": "effect-increasing", "blissInterpretationDeclared": true, "agentA": { "id": "agent-a", "name": "Compound A", "unit": "\u00b5M" }, "agentB": { "id": "agent-b", "name": "Compound B", "unit": "\u00b5M" }, "dosesA": [ 0, 1, 2, 3, 4, 5, 6, 7 ], "dosesB": [ 0, 1, 2, 3, 4, 5, 6, 7 ], "observations": [ { "id": "obs-0-0-0", "doseA": 0, "doseB": 0, "response": 0.0 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0, "doseB": 0, "response": 0.0 }, { "id": "obs-0-0-17", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "obs-0-0-18", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "obs-0-0-19", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "obs-0-0-20", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "obs-0-0-21", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "obs-0-0-22", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "obs-0-0-23", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "obs-0-0-24", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "obs-0-0-25", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "obs-0-0-26", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "obs-0-0-27", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "obs-0-0-28", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "obs-0-0-29", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "obs-0-0-30", "doseA": 0, "doseB": 0, "response": 0.0 }, { "id": "obs-0-0-31", "doseA": 0, "doseB": 0, 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