{"id":"https://openalex.org/W2169352946","doi":"https://doi.org/10.1093/bioinformatics/btg155","title":"A comparison of parametric versus permutationmethods with applications to general and temporalmicroarray gene expression data","display_name":"A comparison of parametric versus permutationmethods with applications to general and temporalmicroarray gene expression data","publication_year":2003,"publication_date":"2003-06-30","ids":{"openalex":"https://openalex.org/W2169352946","doi":"https://doi.org/10.1093/bioinformatics/btg155","mag":"2169352946"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg155","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg155","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/10/1284/449791/btg155.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"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/19/10/1284/449791/btg155.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091189663","display_name":"Ronghui Xu","orcid":"https://orcid.org/0000-0002-2822-0561"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]},{"id":"https://openalex.org/I4210134579","display_name":"Dana-Farber/Harvard Cancer Center","ror":"https://ror.org/03pvyf116","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210117453","https://openalex.org/I4210134579"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ronghui Xu","raw_affiliation_strings":["Department of Biostatistics, Harvard School of Public Health and Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA","Department of Biostatistics, Harvard School\nof Public Health and Dana-Farber Cancer Institute, 44 Binney\nStreet, Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Harvard School of Public Health and Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I4210134579"]},{"raw_affiliation_string":"Department of Biostatistics, Harvard School\nof Public Health and Dana-Farber Cancer Institute, 44 Binney\nStreet, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100413901","display_name":"Xiaochun Li","orcid":"https://orcid.org/0000-0003-0035-4637"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]},{"id":"https://openalex.org/I4210134579","display_name":"Dana-Farber/Harvard Cancer Center","ror":"https://ror.org/03pvyf116","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210117453","https://openalex.org/I4210134579"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaochun Li","raw_affiliation_strings":["Department of Biostatistics, Harvard School of Public Health and Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA","Department of Biostatistics, Harvard School\nof Public Health and Dana-Farber Cancer Institute, 44 Binney\nStreet, Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Harvard School of Public Health and Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I4210134579"]},{"raw_affiliation_string":"Department of Biostatistics, Harvard School\nof Public Health and Dana-Farber Cancer Institute, 44 Binney\nStreet, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I4210117453"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5091189663"],"corresponding_institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I4210134579"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.6646,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.83554261,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"19","issue":"10","first_page":"1284","last_page":"1289"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9901999831199646,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9887999892234802,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/permutation","display_name":"Permutation (music)","score":0.7314980626106262},{"id":"https://openalex.org/keywords/outlier","display_name":"Outlier","score":0.6334950923919678},{"id":"https://openalex.org/keywords/resampling","display_name":"Resampling","score":0.6136643886566162},{"id":"https://openalex.org/keywords/parametric-statistics","display_name":"Parametric statistics","score":0.608425498008728},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.5836808085441589},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5104066729545593},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.49615272879600525},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.484928160905838},{"id":"https://openalex.org/keywords/statistical-hypothesis-testing","display_name":"Statistical hypothesis testing","score":0.4674794375896454},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43618834018707275},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.43288731575012207},{"id":"https://openalex.org/keywords/sample-size-determination","display_name":"Sample size determination","score":0.4166696071624756},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.38207346200942993},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3465263843536377},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3079259693622589},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.273659884929657},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23240268230438232},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22436365485191345},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19257447123527527},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.14973416924476624},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.06749075651168823}],"concepts":[{"id":"https://openalex.org/C21308566","wikidata":"https://www.wikidata.org/wiki/Q7169365","display_name":"Permutation (music)","level":2,"score":0.7314980626106262},{"id":"https://openalex.org/C79337645","wikidata":"https://www.wikidata.org/wiki/Q779824","display_name":"Outlier","level":2,"score":0.6334950923919678},{"id":"https://openalex.org/C150921843","wikidata":"https://www.wikidata.org/wiki/Q1170431","display_name":"Resampling","level":2,"score":0.6136643886566162},{"id":"https://openalex.org/C117251300","wikidata":"https://www.wikidata.org/wiki/Q1849855","display_name":"Parametric statistics","level":2,"score":0.608425498008728},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.5836808085441589},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5104066729545593},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.49615272879600525},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.484928160905838},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.4674794375896454},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43618834018707275},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.43288731575012207},{"id":"https://openalex.org/C129848803","wikidata":"https://www.wikidata.org/wiki/Q2564360","display_name":"Sample size determination","level":2,"score":0.4166696071624756},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.38207346200942993},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3465263843536377},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3079259693622589},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.273659884929657},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23240268230438232},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22436365485191345},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19257447123527527},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.14973416924476624},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.06749075651168823},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","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},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bioinformatics/btg155","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg155","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/10/1284/449791/btg155.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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg155","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg155","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/10/1284/449791/btg155.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":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2169352946.pdf","grobid_xml":"https://content.openalex.org/works/W2169352946.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W162636959","https://openalex.org/W1563982849","https://openalex.org/W1995017987","https://openalex.org/W2038437697","https://openalex.org/W2074089196","https://openalex.org/W2096161760","https://openalex.org/W2105260718","https://openalex.org/W2105494575","https://openalex.org/W2110065044","https://openalex.org/W2114233372","https://openalex.org/W2157795344","https://openalex.org/W4238576781","https://openalex.org/W4240874411","https://openalex.org/W4249966633","https://openalex.org/W4294107304","https://openalex.org/W4300895248"],"related_works":["https://openalex.org/W2021333301","https://openalex.org/W4246719347","https://openalex.org/W2006114390","https://openalex.org/W2380800094","https://openalex.org/W2077508419","https://openalex.org/W2055801436","https://openalex.org/W4385400511","https://openalex.org/W2162206208","https://openalex.org/W2974571879","https://openalex.org/W2507906577"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"In":[2,114,150],"analyses":[3],"of":[4,10,33,53,63,69,140,183],"microarray":[5,64],"data":[6,151],"with":[7,179],"a":[8,30,105],"design":[9],"different":[11],"biological":[12],"conditions,":[13],"ranking":[14,131,156],"genes":[15,34,157],"by":[16,161],"their":[17,54],"differential\u2018":[18],"importance\u2019":[19],"is":[20,134,169],"often":[21,47],"desired":[22],"so":[23],"that":[24,35,98,166],"biologists":[25],"can":[26,158],"focus":[27],"research":[28],"on":[29,77],"small":[31,60],"subset":[32],"are":[36,46,75],"most":[37],"likely":[38],"related":[39],"to":[40,58,121,137,186],"the":[41,59,70,81,88,99,108,138,141,147,153,167,180,190],"experiment":[42],"conditions.":[43],"Permutation":[44],"methods":[45,119,129,185],"recommended":[48],"and":[49,66,93],"used,":[50],"in":[51,80,130,155,189],"place":[52],"parametric":[55,128,175],"counterparts,":[56],"due":[57,136],"sample":[61],"sizes":[62],"experiments":[65],"possible":[67],"non-normality":[68],"data.":[71,191],"The":[72],"recommendations,":[73],"however,":[74],"based":[76],"classical":[78],"knowledge":[79],"hypothesis":[82,91],"test":[83],"setting.":[84],"Results:":[85],"We":[86,96],"explore":[87],"relationship":[89],"between":[90,110],"testing":[92],"gene":[94],"ranking.":[95],"indicate":[97],"permutation":[100,118,142,173,184],"method":[101],"does":[102],"not":[103],"provide":[104],"metric":[106],"for":[107,172],"distance":[109],"two":[111],"underlying":[112],"distributions.":[113],"our":[115],"simulation":[116],"studies":[117],"tend":[120],"be":[122,159,199],"equally":[123],"or":[124],"less":[125],"accurate":[126],"than":[127,174],"genes.":[132],"This":[133],"partially":[135],"discreteness":[139],"distributions,":[143],"as":[144,146],"well":[145],"non-metric":[148],"property.":[149],"analysis":[152],"variability":[154,168],"assessed":[160],"bootstrap.":[162],"It":[163],"turns":[164],"out":[165],"much":[170],"lower":[171],"methods,":[176],"which":[177],"agrees":[178],"known":[181],"robustness":[182],"individual":[187],"outliers":[188],"Contact:":[192],"rxu@jimmy.harvard.edu":[193],"*":[194],"To":[195],"whom":[196],"correspondence":[197],"should":[198],"addressed.":[200]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}