{"id":"https://openalex.org/W1754742998","doi":"https://doi.org/10.1186/1471-2105-7-137","title":"How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results","display_name":"How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results","publication_year":2006,"publication_date":"2006-03-15","ids":{"openalex":"https://openalex.org/W1754742998","doi":"https://doi.org/10.1186/1471-2105-7-137","mag":"1754742998","pmid":"https://pubmed.ncbi.nlm.nih.gov/16539732"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-137","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-137","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-137","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-137","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070435192","display_name":"Frank F. Millenaar","orcid":"https://orcid.org/0009-0002-0880-767X"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Frank F Millenaar","raw_affiliation_strings":["Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands. f.f.millenaar@bio.uu.nl","Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands. f.f.millenaar@bio.uu.nl","institution_ids":["https://openalex.org/I193662353"]},{"raw_affiliation_string":"Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034348182","display_name":"John Okyere","orcid":null},"institutions":[{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"John Okyere","raw_affiliation_strings":["Nottingham Arabidopsis Stock Centre (NASC), Plant Science Division, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK","Nottingham Arabidopsis Stock Centre (NASC), Plant Science Division, University of Nottingham, Loughborough, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nottingham Arabidopsis Stock Centre (NASC), Plant Science Division, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK","institution_ids":["https://openalex.org/I142263535"]},{"raw_affiliation_string":"Nottingham Arabidopsis Stock Centre (NASC), Plant Science Division, University of Nottingham, Loughborough, UK","institution_ids":["https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060653991","display_name":"Sean May","orcid":"https://orcid.org/0000-0001-5282-3250"},"institutions":[{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sean T May","raw_affiliation_strings":["Nottingham Arabidopsis Stock Centre (NASC), Plant Science Division, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK","Nottingham Arabidopsis Stock Centre (NASC), Plant Science Division, University of Nottingham, Loughborough, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nottingham Arabidopsis Stock Centre (NASC), Plant Science Division, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK","institution_ids":["https://openalex.org/I142263535"]},{"raw_affiliation_string":"Nottingham Arabidopsis Stock Centre (NASC), Plant Science Division, University of Nottingham, Loughborough, UK","institution_ids":["https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038167044","display_name":"Martijn van Zanten","orcid":"https://orcid.org/0000-0002-2810-7374"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Martijn van Zanten","raw_affiliation_strings":["Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584, CA, Utrecht, The Netherlands","Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584, CA, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]},{"raw_affiliation_string":"Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022943755","display_name":"Laurentius A. C. J. Voesenek","orcid":"https://orcid.org/0000-0002-3361-3837"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Laurentius ACJ Voesenek","raw_affiliation_strings":["Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584, CA, Utrecht, The Netherlands","Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584, CA, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]},{"raw_affiliation_string":"Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087104498","display_name":"Anton J. M. Peeters","orcid":null},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Anton JM Peeters","raw_affiliation_strings":["Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584, CA, Utrecht, The Netherlands","Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584, CA, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]},{"raw_affiliation_string":"Plant Ecophysiology, Institute of Environmental Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5070435192"],"corresponding_institution_ids":["https://openalex.org/I193662353"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":9.6817,"has_fulltext":true,"cited_by_count":163,"citation_normalized_percentile":{"value":0.98817616,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"7","issue":"1","first_page":"137","last_page":"137"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9811999797821045,"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":0.9811999797821045,"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":0.0038999998942017555,"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.0035000001080334187,"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/dna-microarray","display_name":"DNA microarray","score":0.7230324149131775},{"id":"https://openalex.org/keywords/oligonucleotide","display_name":"Oligonucleotide","score":0.6907109022140503},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6140633821487427},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5169431567192078},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.508018970489502},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4657037854194641},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.45670127868652344},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44757962226867676},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.43264150619506836},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3349921405315399},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32514965534210205},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09942236542701721}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.7230324149131775},{"id":"https://openalex.org/C129312508","wikidata":"https://www.wikidata.org/wiki/Q133686","display_name":"Oligonucleotide","level":3,"score":0.6907109022140503},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6140633821487427},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5169431567192078},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.508018970489502},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4657037854194641},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.45670127868652344},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44757962226867676},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43264150619506836},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3349921405315399},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32514965534210205},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09942236542701721}],"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003657","descriptor_name":"Decision Making","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003657","descriptor_name":"Decision Making","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003657","descriptor_name":"Decision Making","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003657","descriptor_name":"Decision Making","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":"D012680","descriptor_name":"Sensitivity and Specificity","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":"D012680","descriptor_name":"Sensitivity and Specificity","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012986","descriptor_name":"Software Validation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012986","descriptor_name":"Software Validation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012986","descriptor_name":"Software Validation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012986","descriptor_name":"Software Validation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":"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":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000592","qualifier_name":"standards","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},{"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":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-7-137","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-137","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-137","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16539732","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16539732","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:uu:oai:dspace.library.uu.nl:1874/19480","is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/19480","pdf_url":"https://dspace.library.uu.nl/handle/1874/19480","source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 7. NLM (Medline)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:1d8b5962ca014b0584d05b2d84e36d0f","is_oa":true,"landing_page_url":"https://doaj.org/article/1d8b5962ca014b0584d05b2d84e36d0f","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":"BMC Bioinformatics, Vol 7, Iss 1, p 137 (2006)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:169597","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1431565","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1431565","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1431565","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-137","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-137","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-137","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7099999785423279,"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10"}],"awards":[{"id":"https://openalex.org/G1230467146","display_name":null,"funder_award_id":"G17764","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G4035263708","display_name":null,"funder_award_id":"G18881","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G8818745502","display_name":null,"funder_award_id":"BBS/B/1356X","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320321008","display_name":"Universiteit van Amsterdam","ror":"https://ror.org/04dkp9463"},{"id":"https://openalex.org/F4320321010","display_name":"Universiteit Utrecht","ror":"https://ror.org/04pp8hn57"},{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1754742998.pdf","grobid_xml":"https://content.openalex.org/works/W1754742998.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1546962148","https://openalex.org/W1708068686","https://openalex.org/W1964184380","https://openalex.org/W1969172553","https://openalex.org/W1972416794","https://openalex.org/W2015065370","https://openalex.org/W2018673301","https://openalex.org/W2029441111","https://openalex.org/W2037509330","https://openalex.org/W2038437697","https://openalex.org/W2063862573","https://openalex.org/W2070491426","https://openalex.org/W2073205776","https://openalex.org/W2079166554","https://openalex.org/W2096286525","https://openalex.org/W2105025553","https://openalex.org/W2105324766","https://openalex.org/W2107277218","https://openalex.org/W2107491970","https://openalex.org/W2109453886","https://openalex.org/W2109972881","https://openalex.org/W2111033589","https://openalex.org/W2119274294","https://openalex.org/W2120163732","https://openalex.org/W2120865735","https://openalex.org/W2127144561","https://openalex.org/W2127299993","https://openalex.org/W2128312597","https://openalex.org/W2129862056","https://openalex.org/W2130494035","https://openalex.org/W2131531250","https://openalex.org/W2140606663","https://openalex.org/W2141212107","https://openalex.org/W2149548143","https://openalex.org/W2151604722","https://openalex.org/W2168314697","https://openalex.org/W2170989872","https://openalex.org/W2317800347","https://openalex.org/W2608799023","https://openalex.org/W4241639017","https://openalex.org/W4243634040","https://openalex.org/W4247420482"],"related_works":["https://openalex.org/W2097647803","https://openalex.org/W2085475821","https://openalex.org/W2048404795","https://openalex.org/W2034858540","https://openalex.org/W106077234","https://openalex.org/W2041374557","https://openalex.org/W2081929287","https://openalex.org/W2144348650","https://openalex.org/W2132561013","https://openalex.org/W1994852842"],"abstract_inverted_index":{"BACKGROUND:":[0],"Short":[1],"oligonucleotide":[2],"arrays":[3,18],"for":[4,10,206,236,251],"transcript":[5],"profiling":[6],"have":[7,46],"been":[8],"available":[9],"several":[11],"years.":[12],"Generally,":[13],"raw":[14,44],"data":[15,45,77,182],"from":[16,36,224],"these":[17,51],"are":[19,277],"analysed":[20],"with":[21,56,94,178],"the":[22,25,43,60,68,86,108,122,142,148,155,168,174,203,221,225,241,260,264,283,295],"aid":[23],"of":[24,147,220,240,263,282,297],"Microarray":[26],"Analysis":[27],"Suite":[28],"or":[29,34,58],"GeneChip":[30],"Operating":[31],"Software":[32],"(MAS":[33],"GCOS)":[35],"Affymetrix.":[37],"Recently,":[38],"more":[39,57],"methods":[40,52,70,288],"to":[41,66,81,138,197,268,292,303],"analyse":[42],"become":[47],"available.":[48],"Ideally":[49],"all":[50,190],"should":[53],"come":[54],"up":[55],"less":[59],"same":[61,109],"results.":[62,89],"We":[63],"set":[64],"out":[65],"evaluate":[67],"different":[69,96,114,125,143],"and":[71,105,157,172,273],"include":[72],"work":[73],"on":[74,121,183],"our":[75],"own":[76],"set,":[78],"in":[79,113,232,254],"order":[80],"test":[82],"which":[83],"method":[84,123],"gives":[85],"most":[87,169,207,230],"reliable":[88],"RESULTS:":[90],"Calculating":[91],"gene":[92,116],"expression":[93,117,242,249],"6":[95],"algorithms":[97],"(MAS5,":[98],"dChip":[99,101],"PMMM,":[100],"PM,":[102],"RMA,":[103],"GC-RMA":[104],"PDNN)":[106],"using":[107],"(Arabidopsis)":[110],"data,":[111],"results":[112,171,205,229],"calculated":[115,212],"levels.":[118],"Consequently,":[119],"depending":[120],"used,":[124],"genes":[126,184,208,252,276,284,300],"will":[127],"be":[128,290],"identified":[129,185],"as":[130,186],"differentially":[131,187],"regulated.":[132],"Surprisingly,":[133],"there":[134],"was":[135],"only":[136,261],"27":[137],"36%":[139],"overlap":[140],"between":[141,154],"methods.":[144,191],"Furthermore,":[145,215],"47.5%":[146,239],"genes/probe":[149],"sets":[150],"showed":[151,173],"good":[152],"correlation":[153,176],"mismatch":[156,222],"perfect":[158,226],"match":[159,227],"intensities.":[160],"CONCLUSION:":[161],"After":[162],"comparing":[163],"six":[164],"algorithms,":[165],"RMA":[166],"gave":[167],"reproducible":[170],"highest":[175],"coefficients":[177],"Real":[179,200],"Time":[180,201],"RT-PCR":[181],"expressed":[188],"by":[189,199,213,286,301],"However,":[192],"we":[193,216],"were":[194,210],"not":[195],"able":[196],"verify,":[198],"RT-PCR,":[202],"microarray":[204,265],"that":[209,218],"solely":[211],"RMA.":[214],"conclude":[217],"subtraction":[219],"intensity":[223,228],"likely":[231],"a":[233],"significant":[234,248],"underestimation":[235],"at":[237],"least":[238],"values.":[243],"Not":[244],"one":[245],"algorithm":[246],"produced":[247],"values":[250],"present":[253],"quantities":[255],"below":[256],"1":[257],"pmol.":[258],"If":[259],"purpose":[262],"experiment":[266],"is":[267],"find":[269],"new":[270,298],"candidate":[271,299],"genes,":[272],"too":[274],"many":[275],"found,":[278],"then":[279],"mutual":[280],"exclusion":[281],"predicted":[285],"contrasting":[287],"can":[289],"used":[291],"narrow":[293],"down":[294],"list":[296],"64":[302],"73%.":[304]},"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":5},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":10}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}