{"id":"https://openalex.org/W1840387029","doi":"https://doi.org/10.1186/1471-2105-7-23","title":"Evaluation of methods for oligonucleotide array data via quantitative real-time PCR","display_name":"Evaluation of methods for oligonucleotide array data via quantitative real-time PCR","publication_year":2006,"publication_date":"2006-01-17","ids":{"openalex":"https://openalex.org/W1840387029","doi":"https://doi.org/10.1186/1471-2105-7-23","mag":"1840387029","pmid":"https://pubmed.ncbi.nlm.nih.gov/16417622"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-23","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-23","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-23","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/10.1186/1471-2105-7-23","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5106266207","display_name":"Li-Xuan Qin","orcid":null},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Li-Xuan Qin","raw_affiliation_strings":["Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. qinl@mskcc.org","Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. qinl@mskcc.org","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113545732","display_name":"Richard P. Beyer","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard P Beyer","raw_affiliation_strings":["Department of Environmental Health, University of Washington, Box 354695, Seattle, Washington, USA","Department of Environmental Health, University of Washington, Seattle USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Environmental Health, University of Washington, Box 354695, Seattle, Washington, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Environmental Health, University of Washington, Seattle USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I58610484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075015813","display_name":"Francesca N. Hudson","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Francesca N Hudson","raw_affiliation_strings":["Department of Pathology, University of Washington, Box 357705, Seattle, Washington, USA","Department of Pathology, University of Washington Seattle, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Washington, Box 357705, Seattle, Washington, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Pathology, University of Washington Seattle, USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I58610484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002878507","display_name":"Nancy J. Linford","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nancy J Linford","raw_affiliation_strings":["Department of Pathology, University of Washington, Box 357705, Seattle, Washington, USA","Department of Pathology, University of Washington Seattle, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Washington, Box 357705, Seattle, Washington, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Pathology, University of Washington Seattle, USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I58610484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031977112","display_name":"Daryl E. Morris","orcid":"https://orcid.org/0000-0002-1421-5438"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daryl E Morris","raw_affiliation_strings":["Department of Biostatistics, University of Washington, Box 357232, Seattle, Washington, USA","Department of Biostatistics; University of Washington; Seattle USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, University of Washington, Box 357232, Seattle, Washington, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Biostatistics; University of Washington; Seattle USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018100435","display_name":"Kathleen F. Kerr","orcid":"https://orcid.org/0000-0002-6438-9583"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kathleen F Kerr","raw_affiliation_strings":["Department of Biostatistics, University of Washington, Box 357232, Seattle, Washington, USA","Department of Biostatistics; University of Washington; Seattle USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, University of Washington, Box 357232, Seattle, Washington, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Biostatistics; University of Washington; Seattle USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5018100435"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":8.3181,"has_fulltext":true,"cited_by_count":111,"citation_normalized_percentile":{"value":0.98394302,"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":"23","last_page":"23"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.6592000126838684,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.6592000126838684,"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/T10885","display_name":"Gene expression and cancer classification","score":0.22050000727176666,"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":0.0722000002861023,"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/normalization","display_name":"Normalization (sociology)","score":0.7033039331436157},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6391813158988953},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.6063894033432007},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5586028099060059},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5159452557563782},{"id":"https://openalex.org/keywords/gold-standard","display_name":"Gold standard (test)","score":0.5135383605957031},{"id":"https://openalex.org/keywords/oligonucleotide","display_name":"Oligonucleotide","score":0.4383738040924072},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4213528037071228},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30748921632766724},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.26082220673561096},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24707406759262085},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20454123616218567},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.18936744332313538},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14409169554710388}],"concepts":[{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.7033039331436157},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6391813158988953},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.6063894033432007},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5586028099060059},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5159452557563782},{"id":"https://openalex.org/C40993552","wikidata":"https://www.wikidata.org/wiki/Q514654","display_name":"Gold standard (test)","level":2,"score":0.5135383605957031},{"id":"https://openalex.org/C129312508","wikidata":"https://www.wikidata.org/wiki/Q133686","display_name":"Oligonucleotide","level":3,"score":0.4383738040924072},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4213528037071228},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30748921632766724},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.26082220673561096},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24707406759262085},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20454123616218567},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.18936744332313538},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14409169554710388},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D005069","descriptor_name":"Evaluation Studies as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005069","descriptor_name":"Evaluation Studies as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005069","descriptor_name":"Evaluation Studies as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"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":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","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":"D020133","descriptor_name":"Reverse Transcriptase Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020133","descriptor_name":"Reverse Transcriptase Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020133","descriptor_name":"Reverse Transcriptase Polymerase Chain Reaction","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":"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},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-7-23","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-23","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-23","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:16417622","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16417622","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:doaj.org/article:52e89572057f433d878f79f7969ef029","is_oa":false,"landing_page_url":"https://doaj.org/article/52e89572057f433d878f79f7969ef029","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 7, Iss 1, p 23 (2006)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1360686","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1360686","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:10.1186/1471-2105-7-23","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-23","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-23","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":[{"id":"https://openalex.org/G4389057776","display_name":null,"funder_award_id":"P30ES07033","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G4436912372","display_name":null,"funder_award_id":"NIEHS P30ES07033","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"}],"funders":[{"id":"https://openalex.org/F4320308793","display_name":"Fred Hutchinson Cancer Research Center","ror":"https://ror.org/007ps6h72"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1840387029.pdf","grobid_xml":"https://content.openalex.org/works/W1840387029.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1577060935","https://openalex.org/W1606576385","https://openalex.org/W1608062813","https://openalex.org/W1701222854","https://openalex.org/W1969761972","https://openalex.org/W1973614663","https://openalex.org/W2038437697","https://openalex.org/W2041063423","https://openalex.org/W2108244474","https://openalex.org/W2109453886","https://openalex.org/W2109972881","https://openalex.org/W2117517043","https://openalex.org/W2119274294","https://openalex.org/W2120865735","https://openalex.org/W2122598723","https://openalex.org/W2126226510","https://openalex.org/W2160697532","https://openalex.org/W4254259096"],"related_works":["https://openalex.org/W2096302356","https://openalex.org/W2097647803","https://openalex.org/W2085475821","https://openalex.org/W2048404795","https://openalex.org/W2034858540","https://openalex.org/W2069695727","https://openalex.org/W1996185163","https://openalex.org/W2084813257","https://openalex.org/W2045929470","https://openalex.org/W2081127504"],"abstract_inverted_index":{"BACKGROUND:":[0],"There":[1,33],"are":[2,30,54,195,238],"currently":[3],"many":[4],"different":[5],"methods":[6,25,104,113,167,194,217,237,292],"for":[7,71,144,168,230,291,296],"processing":[8,172],"and":[9,26,43,63,92,128,150,181,227,232,244,251,265,268],"summarizing":[10],"probe-level":[11],"data":[12,53,229,258],"from":[13,157,259],"Affymetrix":[14],"oligonucleotide":[15],"arrays.":[16],"It":[17],"is":[18,34,48,138,151,192,300],"of":[19,46,60,77,86,97,171,186,214,257,272,310,316,330],"great":[20],"interest":[21],"to":[22,39,56,154,165,204,319],"validate":[23,166],"these":[24],"identify":[27,212],"those":[28,116],"that":[29,105,117,193,201,218],"most":[31,85,280],"effective.":[32],"no":[35],"single":[36],"best":[37,70,222,322],"way":[38],"do":[40],"this":[41],"validation,":[42],"a":[44,58,75,198,206,269],"variety":[45,59],"approaches":[47],"needed.":[49],"Moreover,":[50],"gene":[51,146],"expression":[52,124,147],"collected":[55,203],"answer":[57],"scientific":[61,207],"questions,":[62],"the":[64,95,119,129,141,169,221,245,279,321,325],"same":[65],"method":[66,271,329],"may":[67],"not":[68],"be":[69],"all":[72],"questions.":[73],"Only":[74],"handful":[76],"validation":[78],"studies":[79,191],"have":[80],"been":[81],"done":[82],"so":[83],"far,":[84],"which":[87,299],"rely":[88],"on":[89,94,197],"spike-in":[90,190],"datasets":[91],"focus":[93],"question":[96],"detecting":[98],"differential":[99],"expression.":[100,110],"Here":[101,160],"we":[102,161,254,287],"seek":[103],"excel":[106],"at":[107],"estimating":[108],"relative":[109],"We":[111,210,307],"evaluate":[112],"by":[114,126,148],"identifying":[115],"give":[118],"strongest":[120],"linear":[121],"association":[122],"between":[123,224],"measurements":[125,164],"array":[127,174,226],"\"gold-standard\"":[130,142],"assay.":[131],"Quantitative":[132],"reverse-transcription":[133],"polymerase":[134],"chain":[135],"reaction":[136],"(qRT-PCR)":[137],"generally":[139,239],"considered":[140],"assay":[143],"measuring":[145],"biologists":[149],"often":[152],"used":[153],"confirm":[155],"findings":[156],"microarray":[158],"data.":[159],"use":[162,256,309],"qRT-PCR":[163],"components":[170],"oligo":[173,225],"data:":[175],"background":[176,273,312],"adjustment,":[177,180],"normalization,":[178],"mismatch":[179,247,260,294,317],"probeset":[182,333],"summary.":[183],"An":[184],"advantage":[185],"our":[187],"approach":[188],"over":[189],"validated":[196],"real":[199],"dataset":[200],"was":[202],"address":[205],"question.":[208],"RESULTS:":[209],"initially":[211],"three":[213,236],"six":[215],"popular":[216],"consistently":[219],"produced":[220],"agreement":[223,302],"RT-PCR":[228],"medium-":[231,250],"high-intensity":[233,252],"genes.":[234],"The":[235],"known":[240],"as":[241,278],"MAS5,":[242],"gcRMA,":[243],"dChip":[246,266],"mode.":[248],"For":[249],"genes,":[253,298],"identified":[255],"probes":[261,295],"(as":[262,275],"in":[263,276,283,301,314],"MAS5":[264],"mismatch)":[267],"sequence-based":[270,311],"adjustment":[274,313,318],"gcRMA)":[277],"important":[281],"factors":[282],"methods'":[284],"performances.":[285],"However,":[286],"found":[288],"poor":[289],"reliability":[290],"using":[293],"low-intensity":[297],"with":[303],"previous":[304],"studies.":[305],"CONCLUSION:":[306],"advocate":[308],"lieu":[315],"achieve":[320],"results":[323],"across":[324],"intensity":[326],"spectrum.":[327],"No":[328],"normalization":[331],"or":[332],"summary":[334],"showed":[335],"any":[336],"consistent":[337],"advantages.":[338]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":10}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}