{"id":"https://openalex.org/W2789415936","doi":"https://doi.org/10.1093/bioinformatics/bty117","title":"Mitigating the adverse impact of batch effects in sample pattern detection","display_name":"Mitigating the adverse impact of batch effects in sample pattern detection","publication_year":2018,"publication_date":"2018-02-27","ids":{"openalex":"https://openalex.org/W2789415936","doi":"https://doi.org/10.1093/bioinformatics/bty117","mag":"2789415936","pmid":"https://pubmed.ncbi.nlm.nih.gov/29506177"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty117","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty117","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/15/2634/25230801/bty117.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/15/2634/25230801/bty117.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100603942","display_name":"Teng Fei","orcid":"https://orcid.org/0000-0001-7888-1715"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Teng Fei","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044128058","display_name":"Tengjiao Zhang","orcid":"https://orcid.org/0000-0001-7815-2504"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tengjiao Zhang","raw_affiliation_strings":["School of Life Sciences and Technology, Tongji University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Sciences and Technology, Tongji University, Shanghai, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101462218","display_name":"Weiyang Shi","orcid":"https://orcid.org/0000-0001-7678-2131"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Weiyang Shi","raw_affiliation_strings":["Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016835023","display_name":"Tianwei Yu","orcid":"https://orcid.org/0000-0003-2502-1628"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tianwei Yu","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA","institution_ids":["https://openalex.org/I150468666"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5016835023","https://openalex.org/A5101462218"],"corresponding_institution_ids":["https://openalex.org/I150468666","https://openalex.org/I59028903"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.0826,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.7626909,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"34","issue":"15","first_page":"2634","last_page":"2641"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.5013999938964844,"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/T10885","display_name":"Gene expression and cancer classification","score":0.5013999938964844,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.1624000072479248,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.13269999623298645,"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/cluster-analysis","display_name":"Cluster analysis","score":0.7474170327186584},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7450389266014099},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.6319040060043335},{"id":"https://openalex.org/keywords/batch-processing","display_name":"Batch processing","score":0.5185297727584839},{"id":"https://openalex.org/keywords/sample-size-determination","display_name":"Sample size determination","score":0.4934369623661041},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.46531060338020325},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.4501478672027588},{"id":"https://openalex.org/keywords/dimension","display_name":"Dimension (graph theory)","score":0.43402621150016785},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22515028715133667},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.19490957260131836},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15747186541557312},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.0696859359741211}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7474170327186584},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7450389266014099},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.6319040060043335},{"id":"https://openalex.org/C172658912","wikidata":"https://www.wikidata.org/wiki/Q661613","display_name":"Batch processing","level":2,"score":0.5185297727584839},{"id":"https://openalex.org/C129848803","wikidata":"https://www.wikidata.org/wiki/Q2564360","display_name":"Sample size determination","level":2,"score":0.4934369623661041},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.46531060338020325},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.4501478672027588},{"id":"https://openalex.org/C33676613","wikidata":"https://www.wikidata.org/wiki/Q13415176","display_name":"Dimension (graph theory)","level":2,"score":0.43402621150016785},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22515028715133667},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.19490957260131836},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15747186541557312},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0696859359741211},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty117","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty117","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/15/2634/25230801/bty117.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29506177","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29506177","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:6061843","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6061843","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty117","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty117","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/15/2634/25230801/bty117.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4300000071525574,"display_name":"Decent work and economic growth","id":"https://metadata.un.org/sdg/8"}],"awards":[{"id":"https://openalex.org/G105336446","display_name":null,"funder_award_id":"NSFC41676119","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3964006637","display_name":null,"funder_award_id":"R01GM124061","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4142563236","display_name":null,"funder_award_id":"R37 AI051231","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G6833642267","display_name":null,"funder_award_id":"U19 AI057266","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G7211878532","display_name":null,"funder_award_id":"R01 GM124061","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7666995241","display_name":null,"funder_award_id":"R37AI051231","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8405245891","display_name":null,"funder_award_id":"U19AI057266","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G868798173","display_name":null,"funder_award_id":"NSFC41476120","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320309381","display_name":"Emory University","ror":"https://ror.org/03czfpz43"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"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"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1986849266","https://openalex.org/W1991909246","https://openalex.org/W2033072655","https://openalex.org/W2033498061","https://openalex.org/W2098831884","https://openalex.org/W2107665951","https://openalex.org/W2116650193","https://openalex.org/W2138398659","https://openalex.org/W2139345901","https://openalex.org/W2160420391","https://openalex.org/W2169353806","https://openalex.org/W2191292005","https://openalex.org/W2211558999","https://openalex.org/W2419478310","https://openalex.org/W2526262591","https://openalex.org/W2598326928","https://openalex.org/W2794891507","https://openalex.org/W3102458540","https://openalex.org/W4235169531"],"related_works":["https://openalex.org/W2161444195","https://openalex.org/W4293088233","https://openalex.org/W2589019771","https://openalex.org/W2985540061","https://openalex.org/W2804364458","https://openalex.org/W4287867321","https://openalex.org/W2496077116","https://openalex.org/W2911183501","https://openalex.org/W2104014222","https://openalex.org/W3006062179"],"abstract_inverted_index":{"Motivation:":[0],"It":[1],"is":[2,33,149],"well":[3],"known":[4],"that":[5],"batch":[6,25,39,44,64,121],"effects":[7,26,40],"exist":[8],"in":[9,49,54,67],"RNA-seq":[10],"data":[11,30,90,128,156],"and":[12,79,136,144],"other":[13],"profiling":[14],"data.":[15,56],"Although":[16],"some":[17],"methods":[18],"do":[19],"a":[20],"good":[21],"job":[22],"adjusting":[23,87],"for":[24],"by":[27],"modifying":[28],"the":[29,38,50,55,63,68,72,88,100,108,119,130,138],"matrices,":[31,91],"it":[32],"still":[34],"difficult":[35],"to":[36,97,118],"remove":[37],"entirely.":[41],"The":[42,146],"remaining":[43],"effect":[45,65,122],"can":[46],"cause":[47],"artifacts":[48],"detection":[51,70],"of":[52,81,86,140],"patterns":[53],"Results:":[57],"In":[58,105,126],"this":[59],"study,":[60],"we":[61,92],"consider":[62],"issue":[66],"pattern":[69],"among":[71],"samples,":[73],"such":[74],"as":[75],"clustering,":[76],"dimension":[77],"reduction":[78],"construction":[80],"networks":[82],"between":[83,103],"subjects.":[84],"Instead":[85],"original":[89],"design":[93],"an":[94],"adaptive":[95],"method":[96,109,124,131],"directly":[98],"adjust":[99],"dissimilarity":[101],"matrix":[102],"samples.":[104],"simulation":[106],"studies,":[107],"achieved":[110],"better":[111],"results":[112],"recovering":[113],"true":[114],"underlying":[115],"clusters,":[116],"compared":[117],"leading":[120],"adjustment":[123],"ComBat.":[125],"real":[127],"analysis,":[129],"effectively":[132],"corrected":[133],"distance":[134],"matrices":[135],"improved":[137],"performance":[139],"clustering":[141],"algorithms.":[142],"Availability":[143],"implementation:":[145],"R":[147],"package":[148],"available":[150,158],"at:":[151],"https://github.com/tengfei-emory/QuantNorm.":[152],"Supplementary":[153,155],"information:":[154],"are":[157],"at":[159],"Bioinformatics":[160],"online.":[161]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
