{ "about": { "fixture": "The plate walk's refit: the worked MTT plate's Compound A without well A9", "ruling": "CSO follow-up of 10 October 2026 on the plate walk, section 2 (3); D-0028 items 2 and 5", "generatedBy": "pipeline/assay-analyser/walk_plate_reference.R", "scriptSha256": "7e5d0aa89e5d9b4a6873c06cda8d314b71b552524b34441268e55a1f628864a7", "referenceRSha256": "912ea05cabc1bd2ddccee30bc815ee09defd3b505ab717c10c4cbfdbc39420f7", "recordedOn": "2026-10-10", "r": "R version 4.3.3 (2024-02-29)", "packages": [ { "name": "drc", "version": "4.0-0" }, { "name": "MASS", "version": "7.3-60.0.1" }, { "name": "jsonlite", "version": "1.8.8" } ], "inputs": { "mttExample": { "file": "pipeline/assay-analyser/fixtures/mtt-example.json", "sha256": "50029b58c869ecb47767215f6b6ba9b54ef33575a77dcd1044cf2c6b3c2a8214" } }, "origin": "The worked MTT plate: synthetic, generated from known parameters with a seeded noise model", "excluded": { "well": "A9", "compound": "Compound A", "concentration_M": 4.57247370827618e-08, "reason": "Example walk: excluded to show the route and its record; no fault in this synthetic reading is claimed." }, "tolerances": { "ruling": "CSO ruling, 6 October 2026", "logIC50": { "absolute": 0.00043, "unit": "log10 units (0.1 percent in concentration)" }, "hill": { "relative": 0.001 }, "topAndBottom": { "absolute": "0.001 x |Top - Bottom|, from the oracle's estimates" }, "waldBoundsLogIC50": { "absolute": 0.0022, "unit": "log10 units (0.5 percent in concentration)" }, "profileBoundsLogIC50": { "absolute": 0.0043, "unit": "log10 units (1 percent in concentration)", "appliesTo": "every finite bound of every fitted curve, withheld values included; the two curves with no finite minimum (expected.minimumAttained false: C30 and MTT Compound C) have no profile to compare" }, "unboundedFlags": "exact, using the oracle's search limit of 10 log10 units each side of the estimate", "objective": { "relative": 1e-06, "note": "the engine's (weighted) residual sum of squares within 1e-6 relative of expected.objective; if the engine's is lower, rerun the oracle" }, "fixedParameters": "exact", "rules": "withheldBy, shown and every count in ruleChecks exact", "notRuled": "The ruling sets no tolerance for F, p, absolute IC50 or Z'; they are arithmetic on the oracle's numbers (suggestion: 1e-6 relative)", "never": "No percentage tolerance on a logarithm" }, "rule": "No value in this file comes from the Drybench engine under test.", "review": { "status": "awaiting the Q-19 reviewer's signature (the CEO names the reviewer)", "reviewer": null, "signedOn": null } }, "normalisation": { "meanVehicle": 1.241875, "meanKill": 0.06, "nVehicle": 8, "nKill": 4 }, "zPrime": { "unchangedByTheExclusion": true, "refused": false, "meanPositive": 1.241875, "meanNegative": 0.06, "sdPositive": 0.0722227457245984, "sdNegative": 0.013589211407093, "nPositive": 8, "nNegative": 4, "zPrime": 0.782180119390736, "belowHalf": false, "sd": "sample standard deviation (n - 1 denominator, R sd()); n shown", "working": "Z' = 1 - 3 (0.072223 + 0.013589) / |1.241875 - 0.060000| = 0.782180 (n = 8 and 4)", "crossCheckPopulationSd": 0.798641663109065 }, "responseEvidence": { "method": "two-sided within-plate rank-trend permutation (Spearman rank covariance), one block, mid-ranks for ties", "statistic": 1892.75, "permutations": 100000, "asExtreme": 0, "p": 9.99990000099999e-06, "generator": "R set.seed(20261010), sample()", "gate": "p < 0.05 reports a midpoint (D-0028 item 2)", "gatePasses": true }, "curve": { "compound": "Compound A", "excludedWell": "A9", "normalised": [ { "well": "A2", "concentration_M": 0.0001, "A570": 0.109, "percentViability": 4.14595452141724 }, { "well": "A3", "concentration_M": 3.33333333333333e-05, "A570": 0.123, "percentViability": 5.33051295610788 }, { "well": "A4", "concentration_M": 1.11111111111111e-05, "A570": 0.212, "percentViability": 12.8609201480698 }, { "well": "A5", "concentration_M": 3.7037037037037e-06, "A570": 0.48, "percentViability": 35.5367530407192 }, { "well": "A6", "concentration_M": 1.23456790123457e-06, "A570": 0.942, "percentViability": 74.6271813855103 }, { "well": "A7", "concentration_M": 4.11522633744856e-07, "A570": 1.026, "percentViability": 81.7345319936541 }, { "well": "A8", "concentration_M": 1.37174211248285e-07, "A570": 1.312, "percentViability": 105.933368588049 }, { "well": "A10", "concentration_M": 1.52415790275873e-08, "A570": 1.333, "percentViability": 107.710206240085 }, { "well": "A11", "concentration_M": 5.08052634252909e-09, "A570": 1.245, "percentViability": 100.264410364886 }, { "well": "B2", "concentration_M": 0.0001, "A570": 0.099, "percentViability": 3.29984135378107 }, { "well": "B3", "concentration_M": 3.33333333333333e-05, "A570": 0.135, "percentViability": 6.34584875727129 }, { "well": "B4", "concentration_M": 1.11111111111111e-05, "A570": 0.208, "percentViability": 12.5224748810153 }, { "well": "B5", "concentration_M": 3.7037037037037e-06, "A570": 0.451, "percentViability": 33.0830248545743 }, { "well": "B6", "concentration_M": 1.23456790123457e-06, "A570": 0.874, "percentViability": 68.8736118455843 }, { "well": "B7", "concentration_M": 4.11522633744856e-07, "A570": 1.05, "percentViability": 83.765203595981 }, { "well": "B8", "concentration_M": 1.37174211248285e-07, "A570": 1.24, "percentViability": 99.8413537810682 }, { "well": "B9", "concentration_M": 4.57247370827618e-08, "A570": 1.209, "percentViability": 97.2184029613961 }, { "well": "B10", "concentration_M": 1.52415790275873e-08, "A570": 1.184, "percentViability": 95.1031200423056 }, { "well": "B11", "concentration_M": 5.08052634252909e-09, "A570": 1.206, "percentViability": 96.9645690111052 }, { "well": "C2", "concentration_M": 0.0001, "A570": 0.099, "percentViability": 3.29984135378107 }, { "well": "C3", "concentration_M": 3.33333333333333e-05, "A570": 0.156, "percentViability": 8.12268640930724 }, { "well": "C4", "concentration_M": 1.11111111111111e-05, "A570": 0.219, "percentViability": 13.4531993654151 }, { "well": "C5", "concentration_M": 3.7037037037037e-06, "A570": 0.445, "percentViability": 32.5753569539926 }, { "well": "C6", "concentration_M": 1.23456790123457e-06, "A570": 0.833, "percentViability": 65.404547858276 }, { "well": "C7", "concentration_M": 4.11522633744856e-07, "A570": 1.086, "percentViability": 86.8112109994712 }, { "well": "C8", "concentration_M": 1.37174211248285e-07, "A570": 1.111, "percentViability": 88.9264939185616 }, { "well": "C9", "concentration_M": 4.57247370827618e-08, "A570": 1.268, "percentViability": 102.210470650449 }, { "well": "C10", "concentration_M": 1.52415790275873e-08, "A570": 1.209, "percentViability": 97.2184029613961 }, { "well": "C11", "concentration_M": 5.08052634252909e-09, "A570": 1.206, "percentViability": 96.9645690111052 } ], "n": 29, "distinctConcentrations": 10, "drcLL4": { "estimates": { "b": 1.25461571826051, "c": 2.87171605664589, "d": 99.3345139867517, "e": 2.11364468659771e-06 }, "standardErrors": { "b": 0.113374451821413, "c": 2.01406479455327, "d": 1.41671169441084, "e": 1.65155814442954e-07 }, "wald": { "b": { "lower": 1.02111666383704, "upper": 1.48811477268398 }, "c": { "lower": -1.27632803547972, "upper": 7.0197601487715 }, "d": { "lower": 96.4167416339761, "upper": 102.252286339527 } }, "dfResidual": 25, "tQuantile": 2.0595385527533, "rss": 431.550848286153, "call": "drm(y ~ conc, data = d, fct = LL.4(fixed = c(NA, NA, NA, NA)), control = drmc(relTol = 1e-12, maxIt = 5000))", "inBriefParameterisation": { "top": 99.3345139867517, "bottom": 2.87171605664589, "logIC50": -5.67496801779463, "hill": -1.25461571826051 }, "note": "cross-check of the minimum only; drc's Wald interval on the linear IC50 scale (e) is never used and not recorded" }, "drcLL24": { "role": "cross-check of the Wald interval on log IC50 only", "call": "drm(..., fct = LL2.4(fixed = ...)): e is log(IC50), natural log", "lnIC50": -13.067098815521, "lnIC50StandardError": 0.0781387349875715, "waldLogIC50": { "lower": -5.74485980689248, "upper": -5.6050780132381 }, "logIC50": -5.67496891006529, "dfResidual": 25 }, "nls": { "estimates": { "top": 99.3345223201865, "bottom": 2.87170962636802, "logIC50": -5.67496813183572, "hill": -1.25461476436555 }, "standardErrors": { "top": 1.39360661994079, "bottom": 2.03014576235496, "logIC50": 0.0343295717295344, "hill": 0.110665398268402 }, "wald": { "top": { "lower": 96.4643357590462, "upper": 102.204708881327 }, "bottom": { "lower": -1.30945383891075, "upper": 7.05287309164679 }, "logIC50": { "lower": -5.7456712083122, "upper": -5.60426505535923 }, "hill": { "lower": -1.48253441855513, "upper": -1.02669511017598 } }, "dfResidual": 25, "tQuantile": 2.0595385527533, "objective": 431.550848285716, "rss": 431.550848285716, "minimumFitted": 3.62940634393027, "startedFrom": "truth", "convergenceTolerance": 1e-06, "earlierAttempts": ["start truth, tol 1e-08: number of iterations exceeded maximum of 1000"], "formula": "y ~ bottom + (top - bottom)/(1 + 10^((logIC50 - x) * hill))", "objectiveIs": "sum((y - f)^2)", "covariance": "(J^T J)^-1 s^2, s^2 = RSS / (n - p)", "profileCrossCheck": { "implementation": "confint(fit, parm = \"logIC50\") on the nls fit restarted at its solution with tol 1e-6 (or 1e-5): MASS's profile t-statistic, spline-interpolated; a cross-check only", "lower": -5.74457657158049, "upper": -5.60403841171303, "lowerUnbounded": false, "upperUnbounded": false, "profiledAtTolerance": 1e-06, "earlierAttempts": [] }, "agreementWithDrc": { "maxRelativeDifference": 2.23917606731867e-06, "logIC50Difference": -1.14041088572492e-07, "objectiveDrcMinusNls": 4.37523794971639e-10 } }, "status": "fitted", "bestFit": { "source": "nls", "estimates": { "top": 99.3345223201865, "bottom": 2.87170962636802, "logIC50": -5.67496813183572, "hill": -1.25461476436555 }, "objective": 431.550848285716, "df": 25, "freeParameters": ["top", "bottom", "logIC50", "hill"], "note": "the lowest objective found by nls or drc LL.4; expected.estimates, the profile, the rules and R squared use it" }, "minimumCheck": { "method": "optim Nelder-Mead then BFGS (reltol 1e-16), ten rounds, from the best fit", "startObjective": 431.550848285716, "polishedObjective": 431.550848285509, "relativeImprovement": 4.78798334842426e-13, "minimumAttained": true, "polishedEstimates": { "top": 99.334519473907, "bottom": 2.87171093855999, "logIC50": -5.67496808300542, "hill": -1.25461508455333 } }, "directProfileLogIC50": { "method": "logIC50 held fixed and the other free parameters refitted; bounds where the objective = minimum x (1 + F(0.95; 1, n - p) / (n - p)), found with uniroot (tol 1e-10) after bracketing in 0.05 log10 steps; unbounded if not reached within 10 log10 units", "objectiveMin": 431.550848285716, "threshold": 504.771201218508, "lower": -5.74457614721793, "upper": -5.60403907892934, "lowerUnbounded": false, "upperUnbounded": false }, "rSquared": 0.990585521941842, "absoluteIC50": { "exists": true, "logAbsoluteIC50": -5.65913120522878, "absoluteIC50_M": 2.19214256447135e-06, "withinTestedRange": true, "formula": "logAbsIC50 = logIC50 - log10((Top - Bottom) / (50 - Bottom) - 1) / Hill", "drcED": 2.19214302258458e-06, "drcEDCall": "ED(drc LL.4 fit, 50, type = \"absolute\") (drc's own estimates)" }, "flatLineFTest": { "reducedModel": "flat line y = mean(y) over the kept wells (one parameter)", "constant": 59.3154506829081, "objectiveFlat": 45839.0625183672, "objectiveFull": 431.550848285716, "weighted": false, "n": 29, "parametersFull": 4, "df1": 3, "df2": 25, "F": 876.82814687341, "p": 1.92377152916516e-25, "alpha": 0.05, "noResponse": false, "working": "F = ((45839.0625 - 431.550848) / 3) / (431.550848 / 25) = 876.828147; p = P(F(3, 25) > F) = 1.92377e-25 (approximate for a nonlinear model)" }, "ruleChecks": { "i": { "distinctConcentrations": 10, "anyConcentrationAtOrBelowZero": false, "fires": false }, "ii": { "p": 1.92377152916516e-25, "fires": false }, "iii": { "concentrationsBelowIC50": 6, "concentrationsAboveIC50": 4, "fires": false }, "iv": { "k": 4.6805, "bendHalfWidthLog10": 0.534261407259775, "plateaus": { "top": { "free": true, "side": "low concentrations", "bendPointLog10": -6.20922953909549, "bendPoint_M": 6.17689844196727e-07, "concentrationsAtOrBeyond": 5, "fires": false }, "bottom": { "free": true, "side": "high concentrations", "bendPointLog10": -5.14070672457594, "bendPoint_M": 7.23258048828827e-06, "concentrationsAtOrBeyond": 3, "fires": false } }, "fires": false }, "v": { "concentrationsPredictedBelow50": 4, "concentrationsPredictedAbove50": 6, "fires": false }, "vi": { "profileWidthLog10": 0.140537068288591, "lowerUnbounded": false, "upperUnbounded": false, "fires": false } }, "expected": { "status": "fitted", "engineMustReport": "a minimum", "minimumAttained": true, "estimates": { "top": 99.3345223201865, "bottom": 2.87170962636802, "logIC50": -5.67496813183572, "hill": -1.25461476436555 }, "freeParameters": ["top", "bottom", "logIC50", "hill"], "fixed": {}, "objective": 431.550848285716, "objectiveIs": "sum((y - f)^2)", "waldLogIC50": { "lower": -5.7456712083122, "upper": -5.60426505535923, "standardError": 0.0343295717295344, "dfResidual": 25, "tQuantile": 2.0595385527533, "source": "nls: logIC50 +/- t(0.975, n - p) x SE, SE from (J^T J)^-1 s^2 at the nls solution" }, "waldNote": null, "profileLogIC50": { "lower": -5.74457614721793, "upper": -5.60403907892934, "lowerUnbounded": false, "upperUnbounded": false }, "flatLineFTest": { "F": 876.82814687341, "p": 1.92377152916516e-25, "df1": 3, "df2": 25, "noResponse": false }, "relativeIC50": { "shown": true, "withheldBy": null, "reason": null, "logIC50": -5.67496813183572, "ic50_M": 2.11364413157728e-06, "poorlyDetermined": false, "poorlyDeterminedReason": null }, "absoluteIC50": { "shown": true, "withheldBy": null, "reason": null, "logAbsoluteIC50": -5.65913120522878, "absoluteIC50_M": 2.19214256447135e-06 } }, "warnings": [] } }