{"id":"https://openalex.org/W2127481171","doi":"https://doi.org/10.1093/bioinformatics/bti479","title":"Answer to the comments of K. Dobbin, J. Shih and R. Simon on the paper 'Evaluation of the gene-specific dye-bias in cDNA microarray experiments'","display_name":"Answer to the comments of K. Dobbin, J. Shih and R. Simon on the paper 'Evaluation of the gene-specific dye-bias in cDNA microarray experiments'","publication_year":2005,"publication_date":"2005-06-07","ids":{"openalex":"https://openalex.org/W2127481171","doi":"https://doi.org/10.1093/bioinformatics/bti479","mag":"2127481171","pmid":"https://pubmed.ncbi.nlm.nih.gov/15941744"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti479","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti479","pdf_url":null,"source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":"letter","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047919662","display_name":"Marie\u2010Laure Martin\u2010Magniette","orcid":"https://orcid.org/0000-0003-4000-9600"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"M.-L. Martin-Magniette","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048149985","display_name":"Julie Aubert","orcid":"https://orcid.org/0000-0001-5203-5748"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. Aubert","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053956743","display_name":"\u00c9ric Cabannes","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"E. Cabannes","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5113487669","display_name":"J.-J. Daudin","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J.-J. Daudin","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5047919662"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.39670704,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.58142741,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"21","issue":"14","first_page":"3065","last_page":"3065"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9994999766349792,"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":0.9994999766349792,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9965999722480774,"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":0.9646999835968018,"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/artifact","display_name":"Artifact (error)","score":0.7575381994247437},{"id":"https://openalex.org/keywords/point","display_name":"Point (geometry)","score":0.5925258994102478},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5545392632484436},{"id":"https://openalex.org/keywords/microarray","display_name":"Microarray","score":0.5267348289489746},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.4486095607280731},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.4479696452617645},{"id":"https://openalex.org/keywords/index","display_name":"Index (typography)","score":0.42771369218826294},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38328123092651367},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3439655303955078},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33542248606681824},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3304872512817383},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26030099391937256},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2574411630630493},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2558189034461975},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20910796523094177},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1865885853767395},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.11581921577453613}],"concepts":[{"id":"https://openalex.org/C2779010991","wikidata":"https://www.wikidata.org/wiki/Q2720909","display_name":"Artifact (error)","level":2,"score":0.7575381994247437},{"id":"https://openalex.org/C28719098","wikidata":"https://www.wikidata.org/wiki/Q44946","display_name":"Point (geometry)","level":2,"score":0.5925258994102478},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5545392632484436},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.5267348289489746},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.4486095607280731},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.4479696452617645},{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.42771369218826294},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38328123092651367},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3439655303955078},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33542248606681824},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3304872512817383},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26030099391937256},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2574411630630493},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2558189034461975},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20910796523094177},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1865885853767395},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.11581921577453613},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005456","descriptor_name":"Fluorescent Dyes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017404","descriptor_name":"In Situ Hybridization, Fluorescence","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008856","descriptor_name":"Microscopy, Fluorescence","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","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":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005456","descriptor_name":"Fluorescent Dyes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017404","descriptor_name":"In Situ Hybridization, Fluorescence","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008856","descriptor_name":"Microscopy, Fluorescence","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","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":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005456","descriptor_name":"Fluorescent Dyes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017404","descriptor_name":"In Situ Hybridization, Fluorescence","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008856","descriptor_name":"Microscopy, Fluorescence","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti479","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti479","pdf_url":null,"source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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:15941744","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15941744","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":2,"referenced_works":["https://openalex.org/W2116616059","https://openalex.org/W2146971344"],"related_works":["https://openalex.org/W52840052","https://openalex.org/W3162837891","https://openalex.org/W1687852313","https://openalex.org/W3029243869","https://openalex.org/W2502336004","https://openalex.org/W1741504538","https://openalex.org/W4308623176","https://openalex.org/W2019696434","https://openalex.org/W2358078963","https://openalex.org/W2023249001"],"abstract_inverted_index":{"We":[0],"would":[1],"like":[2],"to":[3,23,39,85,89,106,131,173,214,280,298,322],"thank":[4],"K.":[5],"Dobbin,":[6],"J.":[7],"Shih":[8],"and":[9,29,52,87,138,150,225,319],"R.":[10],"Simon":[11],"for":[12,156,198],"their":[13,181,258],"comments":[14],"about":[15,31],"Martin-Magniette":[16,68,99,263,291,312],"et":[17,69,100,242,264,269,292,313,336],"al.":[18,70,101,243,265,270,293,314,337],"(2005).":[19],"Their":[20],"remarks":[21,259],"relate":[22],"the":[24,32,49,55,73,95,108,114,175,246,253,283,295,304,353,357,363,366,382,392],"design":[25,321,343],"of":[26,34,54,77,92,166,177,257,311,359,365],"microarray":[27,61],"experiments":[28],"notably":[30],"use":[33,358],"dye-swaps.":[35],"We,":[36],"however,":[37],"want":[38],"make":[40],"it":[41,144,151,170,196,210,328],"clear":[42],"that":[43,127,186,274,339],"our":[44,235],"manuscript":[45],"primarily":[46],"focuses":[47],"on":[48,122,180],"detection,":[50],"quantification":[51],"correction":[53],"gene-specific":[56,218,324],"dye-bias":[57],"introduced":[58],"in":[59,67,98,135,147,193,234,238,262,290,308,349],"dual-color":[60],"experiments.":[62],"The":[63,119,217],"most":[64,91],"important":[65],"point":[66,232],"(2005)":[71,244,271],"is":[72,145,165,205,211,221,288,301,329],"following:":[74],"by":[75,112,303],"dint":[76],"studying":[78],"technical":[79],"errors,":[80],"we":[81,103,184,231,332],"will":[82,369],"be":[83,132,140,154,227,345,370,386],"able":[84,105],"identify":[86],"then":[88],"remove":[90,323],"them.":[93],"For":[94],"first":[96],"time,":[97],"(2005),":[102,338],"were":[104],"quantify":[107],"genespecific":[109,247],"dye":[110,219,248,277,305,325],"bias":[111,179,220,278,306,326],"calculating":[113],"Labelling":[115],"Bias":[116],"Index,":[117],"(LBI).":[118],"LBI":[120],"measured":[121],"different":[123],"array":[124,161,200],"types":[125],"shows":[126],"this":[128,178,203],"artifact":[129,204],"seems":[130],"very":[133],"low":[134],"some":[136,256,350],"cases":[137,149],"could":[139],"thus":[141,153],"neglected.":[142],"However,":[143],"high":[146],"other":[148],"cannot":[152],"neglected":[155],"data":[157],"issued":[158],"from":[159],"these":[160],"types.":[162,201],"This":[163,287],"measure":[164],"crucial":[167],"importance":[168],"as":[169,230],"allows":[171],"users":[172],"evaluate":[174],"impact":[176],"data.":[182],"Moreover,":[183],"think":[185],"each":[187,199],"platform":[188],"should":[189,385],"at":[190],"least":[191],"know":[192],"what":[194],"class":[195],"belongs":[197],"Although":[202,250],"not":[206,222],"lowered":[207],"nor":[208],"understood,":[209],"simply":[212],"dangerous":[213],"underestimate":[215],"it.":[216],"an":[223],"inevitability":[224],"can":[226],"well":[228],"controlled,":[229],"out":[233],"paper.":[236],"Recently,":[237],"another":[239],"paper,":[240],"Dobbin":[241,268,335],"studied":[245],"bias.":[249],"they":[251],"reached":[252],"same":[254],"conclusions,":[255],"are":[260,378],"explained":[261,289],"(2005):":[266,294],"e.g.":[267],"have":[272,281],"found":[273],"\u2018(the":[275],"gene-specific)":[276],"appears":[279],"masked":[282],"true":[284],"differential":[285],"expression\u2019.":[286],"variance":[296],"associated":[297],"a":[299,317,340],"gene":[300],"overestimated":[302],"effect":[307],"model":[309],"(2)":[310],"Dye-swaps":[315],"constitute":[316],"simple":[318],"effective":[320],"when":[327],"high.":[330],"Nevertheless,":[331],"agree":[333],"with":[334],"balanced":[341,375],"block":[342,376],"may":[344],"better":[346],"than":[347],"dye-swaps":[348],"situations.":[351],"As":[352],"former":[354],"designs":[355,377],"allow":[356],"more":[360,371,380],"biological":[361,367],"samples,":[362],"estimation":[364],"variability":[368],"precise.":[372],"Even":[373],"if":[374],"statistically":[379],"efficient,":[381],"following":[383],"considerations":[384],"taken":[387],"into":[388],"account":[389],"before":[390],"choosing":[391],"experimental":[393],"design:":[394]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
