{"id":"https://openalex.org/W2167382937","doi":"https://doi.org/10.1093/bioinformatics/btp363","title":"Comments on the analysis of unbalanced microarray data","display_name":"Comments on the analysis of unbalanced microarray data","publication_year":2009,"publication_date":"2009-06-15","ids":{"openalex":"https://openalex.org/W2167382937","doi":"https://doi.org/10.1093/bioinformatics/btp363","mag":"2167382937","pmid":"https://pubmed.ncbi.nlm.nih.gov/19528084"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp363","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp363","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/16/2035/16889124/btp363.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/25/16/2035/16889124/btp363.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018100435","display_name":"Kathleen F. Kerr","orcid":"https://orcid.org/0000-0002-6438-9583"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kathleen F. Kerr","raw_affiliation_strings":["Department of Biostatistics, Box 357232, University of Washington, Seattle, WA 98195, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Box 357232, University of Washington, Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5018100435"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.1062,"has_fulltext":false,"cited_by_count":59,"citation_normalized_percentile":{"value":0.9474145,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"25","issue":"16","first_page":"2035","last_page":"2041"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9995999932289124,"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/T10885","display_name":"Gene expression and cancer classification","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/T11235","display_name":"Statistical Methods in Clinical Trials","score":0.994700014591217,"subfield":{"id":"https://openalex.org/subfields/2613","display_name":"Statistics and Probability"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11798","display_name":"Optimal Experimental Design Methods","score":0.9794999957084656,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/permutation","display_name":"Permutation (music)","score":0.8525106906890869},{"id":"https://openalex.org/keywords/pooling","display_name":"Pooling","score":0.7471845149993896},{"id":"https://openalex.org/keywords/false-discovery-rate","display_name":"False discovery rate","score":0.7430809736251831},{"id":"https://openalex.org/keywords/null","display_name":"Null (SQL)","score":0.6662881374359131},{"id":"https://openalex.org/keywords/resampling","display_name":"Resampling","score":0.638145387172699},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.6159111857414246},{"id":"https://openalex.org/keywords/multiple-comparisons-problem","display_name":"Multiple comparisons problem","score":0.6130311489105225},{"id":"https://openalex.org/keywords/null-hypothesis","display_name":"Null hypothesis","score":0.607803463935852},{"id":"https://openalex.org/keywords/null-distribution","display_name":"Null distribution","score":0.5023789405822754},{"id":"https://openalex.org/keywords/statistical-hypothesis-testing","display_name":"Statistical hypothesis testing","score":0.49354851245880127},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.4921986162662506},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4632799029350281},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.4537407159805298},{"id":"https://openalex.org/keywords/sample-size-determination","display_name":"Sample size determination","score":0.44876572489738464},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37461555004119873},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.35999980568885803},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35522404313087463},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27843230962753296},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2622103691101074},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22338801622390747},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2212841510772705},{"id":"https://openalex.org/keywords/test-statistic","display_name":"Test statistic","score":0.21641883254051208},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.06824243068695068}],"concepts":[{"id":"https://openalex.org/C21308566","wikidata":"https://www.wikidata.org/wiki/Q7169365","display_name":"Permutation (music)","level":2,"score":0.8525106906890869},{"id":"https://openalex.org/C70437156","wikidata":"https://www.wikidata.org/wiki/Q7228652","display_name":"Pooling","level":2,"score":0.7471845149993896},{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.7430809736251831},{"id":"https://openalex.org/C203763787","wikidata":"https://www.wikidata.org/wiki/Q371029","display_name":"Null (SQL)","level":2,"score":0.6662881374359131},{"id":"https://openalex.org/C150921843","wikidata":"https://www.wikidata.org/wiki/Q1170431","display_name":"Resampling","level":2,"score":0.638145387172699},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.6159111857414246},{"id":"https://openalex.org/C183905921","wikidata":"https://www.wikidata.org/wiki/Q1038757","display_name":"Multiple comparisons problem","level":2,"score":0.6130311489105225},{"id":"https://openalex.org/C191988596","wikidata":"https://www.wikidata.org/wiki/Q628374","display_name":"Null hypothesis","level":2,"score":0.607803463935852},{"id":"https://openalex.org/C120639","wikidata":"https://www.wikidata.org/wiki/Q7068958","display_name":"Null distribution","level":4,"score":0.5023789405822754},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.49354851245880127},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.4921986162662506},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4632799029350281},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.4537407159805298},{"id":"https://openalex.org/C129848803","wikidata":"https://www.wikidata.org/wiki/Q2564360","display_name":"Sample size determination","level":2,"score":0.44876572489738464},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37461555004119873},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.35999980568885803},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35522404313087463},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27843230962753296},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2622103691101074},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22338801622390747},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2212841510772705},{"id":"https://openalex.org/C169857963","wikidata":"https://www.wikidata.org/wiki/Q1461038","display_name":"Test statistic","level":3,"score":0.21641883254051208},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.06824243068695068},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005189","descriptor_name":"False Positive Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005189","descriptor_name":"False Positive Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005189","descriptor_name":"False Positive Reactions","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":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp363","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp363","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/16/2035/16889124/btp363.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:19528084","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19528084","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:2732368","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2732368","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/btp363","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp363","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/16/2035/16889124/btp363.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":0.75,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W181925900","https://openalex.org/W325754011","https://openalex.org/W1509227233","https://openalex.org/W1533335653","https://openalex.org/W1546952499","https://openalex.org/W1548525113","https://openalex.org/W1953115585","https://openalex.org/W1964895626","https://openalex.org/W1965138864","https://openalex.org/W1970920130","https://openalex.org/W1973325935","https://openalex.org/W2009660843","https://openalex.org/W2014245116","https://openalex.org/W2019291952","https://openalex.org/W2021129827","https://openalex.org/W2025604635","https://openalex.org/W2043452927","https://openalex.org/W2065311047","https://openalex.org/W2079711292","https://openalex.org/W2081098333","https://openalex.org/W2092327318","https://openalex.org/W2093902621","https://openalex.org/W2105381419","https://openalex.org/W2110065044","https://openalex.org/W2110891968","https://openalex.org/W2113381189","https://openalex.org/W2123787596","https://openalex.org/W2124758034","https://openalex.org/W2130530904","https://openalex.org/W2134384386","https://openalex.org/W2136781524","https://openalex.org/W2137499573","https://openalex.org/W2137845876","https://openalex.org/W2140954822","https://openalex.org/W2141925314","https://openalex.org/W2147193948","https://openalex.org/W2157795344","https://openalex.org/W2160697532","https://openalex.org/W2165685161","https://openalex.org/W2167809864","https://openalex.org/W2169320928","https://openalex.org/W4294107304","https://openalex.org/W6611113485","https://openalex.org/W6652885914","https://openalex.org/W6655101433"],"related_works":["https://openalex.org/W2467227750","https://openalex.org/W4293336298","https://openalex.org/W2113381189","https://openalex.org/W1995992573","https://openalex.org/W2058846847","https://openalex.org/W2046875666","https://openalex.org/W200550325","https://openalex.org/W2950531074","https://openalex.org/W2342718458","https://openalex.org/W2563586581"],"abstract_inverted_index":{"MOTIVATION:":[0],"Permutation":[1],"testing":[2,31],"is":[3,21],"very":[4,23],"popular":[5,24],"for":[6,140],"analyzing":[7],"microarray":[8],"data":[9],"to":[10,26,74,115,122],"identify":[11],"differentially":[12],"expressed":[13],"(DE)":[14],"genes;":[15],"estimating":[16],"false":[17],"discovery":[18],"rates":[19],"(FDRs)":[20],"a":[22,137],"way":[25],"address":[27],"the":[28,60,76,89],"inherent":[29],"multiple":[30],"problem.":[32],"However,":[33],"combining":[34],"these":[35],"approaches":[36],"may":[37,51,132],"be":[38,53,69,133],"problematic":[39],"when":[40],"sample":[41],"sizes":[42],"are":[43],"unequal.":[44],"RESULTS:":[45],"With":[46],"unbalanced":[47],"data,":[48],"permutation":[49,66,93,109],"tests":[50,67],"not":[52,58],"suitable":[54],"because":[55],"they":[56],"do":[57],"test":[59],"hypothesis":[61],"of":[62,91],"interest.":[63],"In":[64],"addition,":[65],"can":[68,78,98,106],"biased.":[70],"Using":[71],"biased":[72],"P-values":[73,131],"estimate":[75],"FDR":[77],"produce":[79,99],"unacceptable":[80],"bias":[81],"in":[82],"those":[83],"estimates.":[84],"Results":[85],"also":[86],"show":[87],"that":[88,118,129],"approach":[90],"pooling":[92],"null":[94,110],"distributions":[95],"across":[96],"genes":[97,105],"invalid":[100],"P-values,":[101],"since":[102],"even":[103],"non-DE":[104],"have":[107,119],"different":[108],"distributions.":[111],"We":[112],"encourage":[113],"researchers":[114],"use":[116],"statistics":[117],"been":[120],"shown":[121],"reliably":[123],"discriminate":[124],"DE":[125,142],"genes,":[126],"but":[127],"caution":[128],"associated":[130],"either":[134],"invalid,":[135],"or":[136],"less-effective":[138],"metric":[139],"discriminating":[141],"genes.":[143]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":23}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
