{"id":"https://openalex.org/W1608062813","doi":"https://doi.org/10.1186/1471-2105-6-26","title":"Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data","display_name":"Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data","publication_year":2005,"publication_date":"2005-02-10","ids":{"openalex":"https://openalex.org/W1608062813","doi":"https://doi.org/10.1186/1471-2105-6-26","mag":"1608062813","pmid":"https://pubmed.ncbi.nlm.nih.gov/15705192"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-6-26","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-26","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-26","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/10.1186/1471-2105-6-26","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013706483","display_name":"Kerby Shedden","orcid":"https://orcid.org/0000-0001-7222-6664"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210114445","display_name":"Michigan Medicine","ror":"https://ror.org/01zcpa714","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210114445"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kerby Shedden","raw_affiliation_strings":["Department of Statistics, University of Michigan, Ann Arbor, Michigan, USA. kshedden@umich.edu","(University of Michigan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Michigan, Ann Arbor, Michigan, USA. kshedden@umich.edu","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"]},{"raw_affiliation_string":"(University of Michigan)","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100655799","display_name":"Wei Chen","orcid":"https://orcid.org/0000-0001-6048-1860"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Chen","raw_affiliation_strings":["Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA","(University of Michigan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"(University of Michigan)","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059668814","display_name":"Rork Kuick","orcid":"https://orcid.org/0000-0002-8817-5192"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rork Kuick","raw_affiliation_strings":["Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA","(University of Michigan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"(University of Michigan)","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100625252","display_name":"Debashis Ghosh","orcid":"https://orcid.org/0000-0001-6618-1316"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Debashis Ghosh","raw_affiliation_strings":["Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA","(University of Michigan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"(University of Michigan)","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083726660","display_name":"James W. MacDonald","orcid":"https://orcid.org/0000-0002-7328-7626"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210117557","display_name":"Michigan Center for Translational Pathology","ror":"https://ror.org/027t4kk23","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210114445","https://openalex.org/I4210117557"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Macdonald","raw_affiliation_strings":["Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA","(University of Michigan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA","institution_ids":["https://openalex.org/I4210117557","https://openalex.org/I27837315"]},{"raw_affiliation_string":"(University of Michigan)","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031784645","display_name":"Kathleen R. Cho","orcid":"https://orcid.org/0000-0003-0500-9998"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kathleen R Cho","raw_affiliation_strings":["Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA","(University of Michigan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"(University of Michigan)","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077701232","display_name":"Thomas J. Giordano","orcid":"https://orcid.org/0000-0003-0641-8873"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas J Giordano","raw_affiliation_strings":["Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA","(University of Michigan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"(University of Michigan)","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070703103","display_name":"Stephen B. Gruber","orcid":"https://orcid.org/0000-0001-8656-7822"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen B Gruber","raw_affiliation_strings":["Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA","(University of Michigan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"(University of Michigan)","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075652120","display_name":"Eric R. Fearon","orcid":"https://orcid.org/0000-0003-2867-3971"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric R Fearon","raw_affiliation_strings":["Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA","(University of Michigan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"(University of Michigan)","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040007176","display_name":"Jeremy M. G. Taylor","orcid":"https://orcid.org/0000-0003-2791-1229"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy MG Taylor","raw_affiliation_strings":["Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA","(University of Michigan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"(University of Michigan)","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040156444","display_name":"Samir Hanash","orcid":"https://orcid.org/0000-0002-4210-1593"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samir Hanash","raw_affiliation_strings":["Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA","(University of Michigan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"(University of Michigan)","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":11,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":9.4807,"has_fulltext":true,"cited_by_count":127,"citation_normalized_percentile":{"value":0.98788807,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"6","issue":"1","first_page":"26","last_page":"26"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9728999733924866,"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":0.9728999733924866,"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":0.007300000172108412,"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":0.0032999999821186066,"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/profiling","display_name":"Profiling (computer programming)","score":0.6314287185668945},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.6118248701095581},{"id":"https://openalex.org/keywords/false-discovery-rate","display_name":"False discovery rate","score":0.6105598211288452},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5804547071456909},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.548948347568512},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4220202565193176},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.37896665930747986},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35814324021339417},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2841048240661621},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2674468755722046},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1621720790863037}],"concepts":[{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.6314287185668945},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.6118248701095581},{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.6105598211288452},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5804547071456909},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.548948347568512},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4220202565193176},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.37896665930747986},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35814324021339417},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2841048240661621},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2674468755722046},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1621720790863037},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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":"D000704","descriptor_name":"Analysis of Variance","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000704","descriptor_name":"Analysis of Variance","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000704","descriptor_name":"Analysis of Variance","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","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":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011897","descriptor_name":"Random Allocation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011897","descriptor_name":"Random Allocation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011897","descriptor_name":"Random Allocation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015342","descriptor_name":"DNA Probes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015342","descriptor_name":"DNA Probes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015342","descriptor_name":"DNA Probes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015345","descriptor_name":"Oligonucleotide Probes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015345","descriptor_name":"Oligonucleotide Probes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015345","descriptor_name":"Oligonucleotide Probes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000295","qualifier_name":"instrumentation","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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-6-26","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-26","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-26","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:15705192","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15705192","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:oai:deepblue.lib.umich.edu:2027.42/112681","is_oa":true,"landing_page_url":"https://hdl.handle.net/2027.42/112681","pdf_url":"https://hdl.handle.net/2027.42/112681","source":{"id":"https://openalex.org/S4306400393","display_name":"Deep Blue (University of Michigan)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I27837315","host_organization_name":"University of Michigan","host_organization_lineage":["https://openalex.org/I27837315"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:016449cf64bf4b3abf276078f1be14cd","is_oa":false,"landing_page_url":"https://doaj.org/article/016449cf64bf4b3abf276078f1be14cd","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 6, Iss 1, p 26 (2005)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:294040","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC550659","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:550659","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/550659","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:10.1186/1471-2105-6-26","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-26","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-26","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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1608062813.pdf","grobid_xml":"https://content.openalex.org/works/W1608062813.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1611336610","https://openalex.org/W1945743004","https://openalex.org/W1973614663","https://openalex.org/W1991233761","https://openalex.org/W2038437697","https://openalex.org/W2070491426","https://openalex.org/W2074089196","https://openalex.org/W2105381419","https://openalex.org/W2109972881","https://openalex.org/W2119274294","https://openalex.org/W2120865735","https://openalex.org/W2136188920","https://openalex.org/W2157795344","https://openalex.org/W2162871532","https://openalex.org/W2170989872","https://openalex.org/W3124412114","https://openalex.org/W3191599952","https://openalex.org/W4294107304"],"related_works":["https://openalex.org/W2069695727","https://openalex.org/W1996185163","https://openalex.org/W2084813257","https://openalex.org/W2124644189","https://openalex.org/W2043690326","https://openalex.org/W2045929470","https://openalex.org/W4233500668","https://openalex.org/W2081127504","https://openalex.org/W1974145978","https://openalex.org/W1977867163"],"abstract_inverted_index":{"BACKGROUND:":[0],"A":[1],"critical":[2],"step":[3],"in":[4,13,82,123,166,210,279],"processing":[5,39,58,119,237,277,295],"oligonucleotide":[6],"microarray":[7,248],"data":[8,45,62,109,213,258,269],"is":[9,72],"combining":[10],"the":[11,24,48,107,118,124,145,167,199,211,228],"information":[12],"multiple":[14,35],"probes":[15],"to":[16,114,142,178,181],"produce":[17,182],"a":[18,28,130,159,179,204,240],"single":[19],"number":[20,125,161],"that":[21],"best":[22,137],"captures":[23],"expression":[25,245],"level":[26],"of":[27,84,126,144,162,172,195,198,236,247,275],"RNA":[29],"transcript.":[30],"Several":[31],"systematic":[32],"studies":[33,286],"comparing":[34,293],"methods":[36,59,120,139,201,219,231,278],"for":[37,50,56,66,77,92,100,227],"array":[38,276],"have":[40],"used":[41],"tightly":[42,255],"controlled":[43,256],"calibration":[44,257],"sets":[46,63,110,214,259],"as":[47],"basis":[49],"comparison.":[51],"Here":[52],"we":[53],"compare":[54],"performances":[55],"seven":[57,200],"using":[60,254,268],"two":[61,85,108,197,212],"originally":[64],"collected":[65],"disease":[67,280],"profiling":[68,281],"studies.":[69],"An":[70],"emphasis":[71],"placed":[73],"on":[74,191,243],"understanding":[75],"sensitivity":[76],"detecting":[78],"differentially":[79,102,148],"expressed":[80,94,103],"genes":[81,127,147],"terms":[83],"key":[86],"statistical":[87],"determinants:":[88],"test":[89,97,153,164,185],"statistic":[90,98,186],"variability":[91],"non-differentially":[93],"genes,":[95],"and":[96,157,203,221,282],"size":[99],"truly":[101],"genes.":[104],"RESULTS:":[105],"In":[106],"considered":[111,215],"here,":[112],"up":[113,141],"seven-fold":[115],"variation":[116],"across":[117],"was":[121,175],"found":[122],"detected":[128],"at":[129],"given":[131,289],"false":[132],"discovery":[133],"rate":[134],"(FDR).":[135],"The":[136],"performing":[138],"called":[140],"90%":[143],"same":[146],"expressed,":[149],"had":[150,158],"less":[151],"variable":[152,184],"statistics":[154,165],"under":[155,188],"randomization,":[156],"greater":[160,290],"large":[163],"experimental":[168],"data.":[169,249],"Poor":[170],"performance":[171,252],"one":[173],"method":[174,238],"directly":[176],"tied":[177],"tendency":[180],"highly":[183,262],"values":[187],"randomization.":[189],"Based":[190],"an":[192],"overall":[193],"measure":[194],"performance,":[196],"(Dchip":[202],"trimmed":[205],"mean":[206],"approach)":[207],"are":[208,223,232,260],"superior":[209],"here.":[216],"Two":[217],"other":[218,229,283],"(MAS5":[220],"GCRMA-EB)":[222],"inferior,":[224],"while":[225],"results":[226,265],"three":[230],"mixed.":[233],"CONCLUSIONS:":[234],"Choice":[235],"has":[239],"major":[241],"impact":[242],"differential":[244],"analysis":[246],"Previously":[250],"reported":[251,266],"analyses":[253],"not":[261],"consistent":[263],"with":[264],"here":[267],"from":[270],"human":[271],"tissue":[272],"samples.":[273],"Performance":[274],"realistic":[284],"biological":[285],"should":[287],"be":[288],"consideration":[291],"when":[292],"Affymetrix":[294],"methods.":[296]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":4}],"updated_date":"2026-06-18T10:00:31.954636","created_date":"2025-10-10T00:00:00"}