{"id":"https://openalex.org/W4388822267","doi":"https://doi.org/10.1371/journal.pcbi.1011659","title":"Addressing erroneous scale assumptions in microbe and gene set enrichment analysis","display_name":"Addressing erroneous scale assumptions in microbe and gene set enrichment analysis","publication_year":2023,"publication_date":"2023-11-20","ids":{"openalex":"https://openalex.org/W4388822267","doi":"https://doi.org/10.1371/journal.pcbi.1011659","pmid":"https://pubmed.ncbi.nlm.nih.gov/37983251"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011659","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011659","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011659&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011659&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067693539","display_name":"Kyle C. McGovern","orcid":"https://orcid.org/0000-0002-8945-1777"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyle C. McGovern","raw_affiliation_strings":["Program in Bioinformatics and Genomics, Pennsylvania State University, State College, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program in Bioinformatics and Genomics, Pennsylvania State University, State College, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059360789","display_name":"Michelle Pistner Nixon","orcid":null},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michelle Pistner Nixon","raw_affiliation_strings":["College of Information Sciences and Technology, Pennsylvania State University, State College, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Sciences and Technology, Pennsylvania State University, State College, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083571585","display_name":"Justin D. Silverman","orcid":"https://orcid.org/0000-0002-3063-2098"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Justin D. Silverman","raw_affiliation_strings":["College of Information Sciences and Technology, Pennsylvania State University, State College, Pennsylvania, United States of America","Departments of Medicine and Statistics, Pennsylvania State University, State College, Pennsylvania, United States of America","Institute for Computational and Data Science, Pennsylvania State University, State College, Pennsylvania, United States of America","Program in Bioinformatics and Genomics, Pennsylvania State University, State College, Pennsylvania, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-3063-2098","affiliations":[{"raw_affiliation_string":"College of Information Sciences and Technology, Pennsylvania State University, State College, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Departments of Medicine and Statistics, Pennsylvania State University, State College, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Institute for Computational and Data Science, Pennsylvania State University, State College, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Program in Bioinformatics and Genomics, Pennsylvania State University, State College, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5083571585"],"corresponding_institution_ids":["https://openalex.org/I130769515"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.1075,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.76482614,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"19","issue":"11","first_page":"e1011659","last_page":"e1011659"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9911999702453613,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.6721528768539429},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6652336716651917},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.6486958861351013},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5739314556121826},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.549321174621582},{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.5476341843605042},{"id":"https://openalex.org/keywords/suspect","display_name":"Suspect","score":0.5024130344390869},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.43676093220710754},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4241424798965454},{"id":"https://openalex.org/keywords/level-of-measurement","display_name":"Level of measurement","score":0.4230906665325165},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.41178175806999207},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3773607313632965},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.27153438329696655},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.255718857049942},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20949843525886536},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11292371153831482}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.6721528768539429},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6652336716651917},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.6486958861351013},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5739314556121826},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.549321174621582},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.5476341843605042},{"id":"https://openalex.org/C2778223634","wikidata":"https://www.wikidata.org/wiki/Q224952","display_name":"Suspect","level":2,"score":0.5024130344390869},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.43676093220710754},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4241424798965454},{"id":"https://openalex.org/C55786151","wikidata":"https://www.wikidata.org/wiki/Q951437","display_name":"Level of measurement","level":2,"score":0.4230906665325165},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.41178175806999207},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3773607313632965},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.27153438329696655},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.255718857049942},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20949843525886536},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11292371153831482},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1011659","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011659","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011659&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:37983251","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37983251","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10695402","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10695402","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10695402/pdf/pcbi.1011659.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1011659","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011659","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:b3e581c803374323b61ca0d03b08349c","is_oa":true,"landing_page_url":"https://doaj.org/article/b3e581c803374323b61ca0d03b08349c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 11, p e1011659 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011659","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011659","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011659&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1185693225","display_name":null,"funder_award_id":"T32 GM145449","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1870429759","display_name":null,"funder_award_id":"T32GM102057","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2094686404","display_name":null,"funder_award_id":"1R01GM148972-01","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3446691354","display_name":null,"funder_award_id":"NIH 1R01GM148972-01","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4355105991","display_name":null,"funder_award_id":"R01 GM148972","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G457231415","display_name":"Computation, Bioinformatics, and Statistics (CBIOS) Training Program","funder_award_id":"2t32gm102057-06","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5910873537","display_name":null,"funder_award_id":"5T32GM102057","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6028199925","display_name":null,"funder_award_id":"5 T32 GM102057-10","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8512934175","display_name":"DMS/NIGMS 1: Addressing Measurement Limitations for Sequence Count Data","funder_award_id":"1r01gm148972-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4388822267.pdf","grobid_xml":"https://content.openalex.org/works/W4388822267.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1513838499","https://openalex.org/W1569946922","https://openalex.org/W2010457001","https://openalex.org/W2018433132","https://openalex.org/W2018838463","https://openalex.org/W2055708265","https://openalex.org/W2107018762","https://openalex.org/W2112220625","https://openalex.org/W2130410032","https://openalex.org/W2130879249","https://openalex.org/W2133998111","https://openalex.org/W2137409194","https://openalex.org/W2152239989","https://openalex.org/W2156631105","https://openalex.org/W2156975150","https://openalex.org/W2161577298","https://openalex.org/W2179438025","https://openalex.org/W2214074259","https://openalex.org/W2516350521","https://openalex.org/W2766676715","https://openalex.org/W2769542288","https://openalex.org/W2770269406","https://openalex.org/W2912712397","https://openalex.org/W2949960840","https://openalex.org/W2951061751","https://openalex.org/W2953116118","https://openalex.org/W2962821542","https://openalex.org/W2964312306","https://openalex.org/W3000731297","https://openalex.org/W3013332389","https://openalex.org/W3039150496","https://openalex.org/W3105672003","https://openalex.org/W3112665264","https://openalex.org/W3175720304","https://openalex.org/W3181823224","https://openalex.org/W4280534380"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W3197016913","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2000169967"],"abstract_inverted_index":{"By":[0],"applying":[1],"Differential":[2],"Set":[3],"Analysis":[4],"(DSA)":[5],"to":[6,49,91,115,122,146,194,213,229,236,242],"sequence":[7,23,226],"count":[8,24,227],"data,":[9],"researchers":[10,191],"can":[11,89,142,192,234],"determine":[12],"whether":[13,196],"groups":[14],"of":[15,40,178,209,220,225],"microbes":[16],"or":[17],"genes":[18],"are":[19,120,128,199],"differentially":[20],"enriched.":[21],"Yet":[22],"data":[25,32,52],"suffer":[26],"from":[27,202],"a":[28,111,155,164,183],"scale":[29,37,87,170,179,204,221,232,249],"limitation:":[30],"these":[31,51,86],"lack":[33],"information":[34],"about":[35,74],"the":[36,41,75,176,207,218],"(i.e.,":[38,54],"size)":[39],"biological":[42],"system":[43,77],"under":[44],"study,":[45],"leading":[46],"some":[47],"authors":[48],"call":[50],"compositional":[53],"proportional).":[55],"In":[56],"this":[57,101,134,210],"article,":[58],"we":[59,103,109,153,173],"show":[60,80,244],"that":[61,66,81,158,190,231,245],"commonly":[62],"used":[63],"DSA":[64],"methods":[65],"rely":[67],"on":[68,182],"normalization":[69],"make":[70],"strong,":[71],"implicit":[72],"assumptions":[73,88],"unmeasured":[76],"scale.":[78],"We":[79],"even":[82],"small":[83],"errors":[84,124,168,238],"in":[85,169,223,239],"lead":[90,235],"positive":[92],"predictive":[93],"values":[94],"as":[95,97],"low":[96],"9%.":[98],"To":[99],"address":[100],"problem,":[102],"take":[104],"three":[105],"novel":[106],"approaches.":[107],"First,":[108],"introduce":[110,154],"sensitivity":[112],"analysis":[113],"framework":[114,135],"identify":[116],"when":[117,126],"modeling":[118],"results":[119],"robust":[121],"such":[123],"and":[125,141,149,187,247],"they":[127],"suspect.":[129],"Unlike":[130],"standard":[131],"benchmarking":[132],"studies,":[133],"does":[136],"not":[137],"require":[138],"ground-truth":[139],"knowledge":[140],"therefore":[143],"be":[144],"applied":[145],"both":[147],"simulated":[148],"real":[150],"data.":[151],"Second,":[152],"statistical":[156],"test":[157],"provably":[159],"controls":[160],"Type-I":[161],"error":[162],"at":[163,200],"nominal":[165],"rate":[166],"despite":[167],"assumptions.":[171,205],"Finally,":[172],"discuss":[174],"how":[175],"impact":[177,219],"limitations":[180,222,233],"depends":[181],"researcher's":[184],"scientific":[185],"goals":[186,198],"provide":[188],"tools":[189],"use":[193],"evaluate":[195],"their":[197],"risk":[201],"erroneous":[203],"Overall,":[206],"goal":[208],"article":[211],"is":[212,252],"catalyze":[214],"future":[215],"research":[216],"into":[217],"analyses":[224],"data;":[228],"illustrate":[230],"inferential":[237],"practice;":[240],"yet":[241],"also":[243],"rigorous":[246],"reproducible":[248],"reliant":[250],"inference":[251],"possible":[253],"if":[254],"done":[255],"carefully.":[256]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
