{"id":"W4416647692","doi":"10.5256/f1000research.5001.r5620","title":"Referee report. For: shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R [v1; indexed, http://f1000r.es/3ux]","year":2014,"lang":"en","type":"article","venue":"Faculty of 1000 Research Ltd","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":false,"ca_institutions":"","funders":"Natural Sciences and Engineering Research Council of Canada; Johns Hopkins University","keywords":"DNA methylation; Quality (philosophy); DNA; Methylation; Epigenetics; Control (management)","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.007755289,0.0002077036,0.0004925716,0.0002698837,0.00008944829,0.00002406242,0.0003766491,0.0003586762,0.00001964776],"category_scores_gemma":[0.006904264,0.0001960346,0.0002035777,0.0002962592,0.0002856835,0.00001877701,0.000147476,0.000341221,0.000005108726],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007696609,"about_ca_system_score_gemma":0.0001921969,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005069653,"about_ca_topic_score_gemma":0.0005365591,"domain_scores_codex":[0.9962007,0.001089788,0.0008703456,0.0005985435,0.0007845373,0.0004560371],"domain_scores_gemma":[0.9961243,0.000619535,0.0005086995,0.0007307537,0.001887366,0.0001293231],"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":[0.0007634605,0.0001848223,0.009548534,0.0001351191,0.0000863006,0.000001709136,0.0003129316,0.0002610614,0.9773025,0.001238913,0.0003273605,0.009837317],"study_design_scores_gemma":[0.001891296,0.0009051349,0.03800653,0.00007497336,0.00001728695,0.000001263053,0.0003480177,0.0005240543,0.911026,0.002999977,0.04397339,0.000232056],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9365621,0.0003179057,0.0591078,0.001142864,0.00009969573,0.0007333117,0.0002867355,0.000008800149,0.001740842],"genre_scores_gemma":[0.9948774,0.00009125087,0.002284616,0.00001874526,0.0001439386,0.00008095559,0.001172303,0.00003112122,0.001299674],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06627645,"threshold_uncertainty_score":0.8265548,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05064091801667391,"score_gpt":0.3979727412155875,"score_spread":0.3473318231989135,"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."}}