{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29881472", "kind": "science-record", "revision": 4, "content_hash": "sha256:c75db4ab585f199197647ee90092fd9233d6c3df2557308dca26febb0c328c84", "created_at": "2026-11-01T15:40:34Z", "updated_at": "2026-11-01T21:21:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying mislabeled and contaminated DNA methylation microarray data: an extended quality control toolset with examples from GEO.", "doi": "10.1186/s13148-018-0504-1", "pmid": "29881472", "authors": ["Jonathan A Heiss", "Allan C Just"], "journal": "Clinical epigenetics", "year": 2018, "abstract": "Background: Mislabeled, contaminated or poorly performing samples can threaten power in methylation microarray analyses or even result in spurious associations. We describe a set of quality checks for the popular Illumina 450K and EPIC microarrays to identify problematic samples and demonstrate their application in publicly available datasets.\nMethods: Quality checks implemented here include 17 control metrics defined by the manufacturer, a sex check to detect mislabeled sex-discordant samples, and both an identity check for fingerprinting sample donors and a measure of sample contamination based on probes querying high-frequency SNPs. These checks were tested on 80 datasets comprising 8327 samples run on the 450K microarray from the GEO repository.\nResults: Nine hundred forty samples were flagged by at least one control metric and 133 samples from 20 datasets were assigned the wrong sex. In a dataset in which a subset of samples appear contaminated with a single source of DNA, we demonstrate that our measure based on outliers among SNP probes was strongly correlated (> 0.95) with another independent measure of contamination.\nConclusions: A more complete examination of samples that may be mislabeled, contaminated, or have poor performance due to technical problems will improve downstream analyses and replication of findings. We demonstrate that quality control problems are prevalent in a public repository of DNA methylation data. We advocate for a more thorough quality control workflow in epigenome-wide association studies and provide a software package to perform the checks described in this work. Reproducible code and supplementary material are available at 10.5281/zenodo.1172730.", "claims": [{"id": "claim-method", "statement": "The parameters were estimated using the Metropolis algorithm implemented in the Julia programming language (code is provided the supplement).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29881472", "locator": "sections[5] \"Quality checks\" paragraph 8", "quote": "The parameters were estimated using the Metropolis algorithm implemented in the Julia programming language (code is provided the supplement)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "R and Julia code to reproduce all analyses and results presented here, including retrieval of public methylation datasets, as well as other supplementary material, are available at 10.5281/zenodo.1172730. The ewastools R package can be found at https://github.com/hhhh5/ewastools.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29881472", "locator": "sections[11] \"Availability of data and materials\" paragraph 2", "quote": "R and Julia code to reproduce all analyses and results presented here, including retrieval of public methylation datasets, as well as other supplementary material, are available at 10.5281/zenodo.1172730. The ewastools R package can be found at https://github.com/hhhh5/ewastools."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper applied an ewastools statistical quality-control workflow to 80 public GEO 450K datasets comprising 8,327 samples and found that 940 samples were flagged by at least one manufacturer control metric, while 133 samples from 20 datasets had the wrong recorded sex.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29881472", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We describe a set of quality checks for the popular Illumina 450K and EPIC microarrays to identify problematic samples and demonstrate their application in publicly available datasets."}, {"asset": "source:pmid:29881472", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "These checks were tested on 80 datasets comprising 8327 samples run on the 450K microarray from the GEO repository."}, {"asset": "source:pmid:29881472", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Nine hundred forty samples were flagged by at least one control metric and 133 samples from 20 datasets were assigned the wrong sex."}, {"asset": "source:pmid:29881472", "locator": "sections[6] \"Results\" paragraph 2", "quote": "Overall, 940 samples (11%) from 41 datasets (51%) were flagged by at least one of the 17 metrics in control_metrics, leaving 7387 samples that passed this first check."}, {"asset": "source:pmid:29881472", "locator": "sections[6] \"Results\" paragraph 7", "quote": "The function check_sex estimated that 133 of the 8327 samples had been assigned the wrong sex yielding an error rate of 1.6%, with 13 cases being unclear, as the inferred sex was discordant between T¯nX and T¯nY (Fig. 3a). Of the 80 datasets, 20 (25%) contained these sex-mismatched samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper applied an ewastools statistical quality-control workflow to 80 public GEO 450K datasets comprising 8,327 samples and found that 940 samples were flagged by at least one manufacturer control metric, while 133 samples from 20 datasets had the wrong recorded sex.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:29881472"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29881472", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13148-018-0504-1", "sha256": "sha256:edfbdaa5d8e14fd7677d4c4203decd509ce6476331fad0e15906275b3fc57183", "bytes": 37880, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13148-018-0504-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5984806", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:29881472:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:571213a2821962221cc5f4c48241d28e5baefd55d8d44fba4823148cc82ab4c0", "bytes": 1053, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#Tab1", "version": null, "note": "Summary of the number of samples flagged by each of the 17 control metrics outlined in the BeadArray controls reporter software guide. n.a.—not available", "structure": {"pmcid": "PMC5984806", "section_index": 6, "section_title": "Results", "row_count": 19, "column_count": 4}, "table": {"label": "Table 1", "caption": "Summary of the number of samples flagged by each of the 17 control metrics outlined in the BeadArray controls reporter software guide. n.a.—not available", "rows": [["Metric", "Passed", "Flagged", "n.a."], ["Restoration", "8326", "0", "1"], ["Staining green", "7885", "10", "432"], ["Staining red", "7764", "14", "549"], ["Extension green", "8324", "3", "0"], ["Extension red", "8326", "1", "0"], ["Hybridization high/medium", "8326", "1", "0"], ["Hybridization medium/low", "8327", "0", "0"], ["Target removal 1", "8327", "0", "0"], ["Target removal 2", "8327", "0", "0"], ["Bisulfite conversion I green", "8317", "10", "0"], ["Bisulfite conversion I red", "8208", "119", "0"], ["Bisulfite conversion II", "7950", "377", "0"], ["Specificity I green", "8323", "4", "0"], ["Specificity I red", "8279", "48", "0"], ["Specificity II", "8326", "1", "0"], ["Non-polymorphic green", "7677", "558", "92"], ["Non-polymorphic red", "7917", "318", "92"], ["Any of the above", "7387", "940", "–"]], "row_count": 19, "column_count": 4, "numeric_cells": 55, "header_rows": 1, "locator": "section[6]/table-wrap[1]#Tab1"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Metropolis algorithm", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The parameters were estimated using the Metropolis algorithm implemented in the Julia programming language (code is provided the supplement)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Metropolis algorithm), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T03:47:04+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. 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