{"id":"W4313643069","doi":"10.1186/s13072-022-00477-0","title":"Who’s afraid of the X? Incorporating the X and Y chromosomes into the analysis of DNA methylation array data","year":2023,"lang":"en","type":"article","venue":"Epigenetics & Chromatin","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":29,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Children's Hospital; University of British Columbia","funders":"Canadian Institutes of Health Research; BC Children's Hospital","keywords":"Biology; Epigenome; Genetics; DNA methylation; Normalization (sociology); Y chromosome; X chromosome; Chromosome; Computational biology; Gene","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001265005,0.0001536176,0.0002473946,0.00008746789,0.0002296768,0.00003096793,0.0007411735,0.0001103584,0.000007716169],"category_scores_gemma":[0.0004805505,0.00008623821,0.0001139021,0.00108765,0.000342907,0.000005999746,0.0005570175,0.0000930079,9.813419e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000007283877,"about_ca_system_score_gemma":0.00007997271,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009903483,"about_ca_topic_score_gemma":0.00045313,"domain_scores_codex":[0.9983907,0.0003105754,0.0005012281,0.0003249015,0.0003125439,0.0001600439],"domain_scores_gemma":[0.9977269,0.0002040651,0.0004888293,0.001427391,0.0001201969,0.00003261656],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.000005569906,0.00001587779,0.01518029,0.00002888295,0.0003567575,1.098027e-7,0.0009817204,0.002887358,0.974333,0.0001259814,0.0001165658,0.005967826],"study_design_scores_gemma":[0.0001423951,0.00007025761,0.2087112,0.00002020867,0.0003971747,2.537967e-7,0.0004165206,0.01096917,0.7767704,0.0009020444,0.0014794,0.0001209557],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9936756,0.002997816,0.001928288,0.0007332492,0.00009987272,0.0002730913,0.00007817493,0.000007752254,0.0002061134],"genre_scores_gemma":[0.9974983,0.0009366924,0.0009809315,0.00003980281,0.0001002036,0.00001271751,0.0002879974,0.00001932551,0.0001240021],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1975626,"threshold_uncertainty_score":0.3516692,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02457626042812939,"score_gpt":0.2880626704228323,"score_spread":0.263486409994703,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}