{"id":"https://openalex.org/W2103727721","doi":"https://doi.org/10.1093/bioinformatics/bti617","title":"Accounting for probe-level noise in principal component analysis of microarray data","display_name":"Accounting for probe-level noise in principal component analysis of microarray data","publication_year":2005,"publication_date":"2005-08-09","ids":{"openalex":"https://openalex.org/W2103727721","doi":"https://doi.org/10.1093/bioinformatics/bti617","mag":"2103727721","pmid":"https://pubmed.ncbi.nlm.nih.gov/16091409"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti617","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti617","pdf_url":null,"source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017674487","display_name":"Guido Sanguinetti","orcid":"https://orcid.org/0000-0002-6663-8336"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"G. Sanguinetti","raw_affiliation_strings":["Department of Computer Science, Regent Court 211 Portobello Road, Sheffield S1 4DP, UK","Department of Computer Science, Regent Court, 211 Portobello Road, Sheffield, S1 4DP, UK#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Regent Court 211 Portobello Road, Sheffield S1 4DP, UK","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, Regent Court, 211 Portobello Road, Sheffield, S1 4DP, UK#TAB#","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030562190","display_name":"Marta Milo","orcid":"https://orcid.org/0000-0002-6996-6431"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"M. Milo","raw_affiliation_strings":["Department of Computer Science, Regent Court, 211 Portobello Road, Sheffield, S1 4DP, UK#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Regent Court, 211 Portobello Road, Sheffield, S1 4DP, UK#TAB#","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023995814","display_name":"Magnus Rattray","orcid":"https://orcid.org/0000-0001-8196-5565"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"M. Rattray","raw_affiliation_strings":["School Of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK"],"affiliations":[{"raw_affiliation_string":"School Of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023849469","display_name":"Neil D. Lawrence","orcid":"https://orcid.org/0000-0001-9258-1030"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"N. D. Lawrence","raw_affiliation_strings":["Department of Computer Science, Regent Court, 211 Portobello Road, Sheffield, S1 4DP, UK#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Regent Court, 211 Portobello Road, Sheffield, S1 4DP, UK#TAB#","institution_ids":["https://openalex.org/I91136226"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5017674487"],"corresponding_institution_ids":["https://openalex.org/I91136226"],"apc_list":null,"apc_paid":null,"fwci":2.6583,"has_fulltext":false,"cited_by_count":58,"citation_normalized_percentile":{"value":0.89916414,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"21","issue":"19","first_page":"3748","last_page":"3754"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9940000176429749,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.9933000206947327,"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/principal-component-analysis","display_name":"Principal component analysis","score":0.8118230700492859},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.5822973847389221},{"id":"https://openalex.org/keywords/component","display_name":"Component (thermodynamics)","score":0.5466362833976746},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5292118191719055},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4349881410598755},{"id":"https://openalex.org/keywords/accounting","display_name":"Accounting","score":0.4098206162452698},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19076067209243774},{"id":"https://openalex.org/keywords/business","display_name":"Business","score":0.1033291220664978}],"concepts":[{"id":"https://openalex.org/C27438332","wikidata":"https://www.wikidata.org/wiki/Q2873","display_name":"Principal component analysis","level":2,"score":0.8118230700492859},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.5822973847389221},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.5466362833976746},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5292118191719055},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4349881410598755},{"id":"https://openalex.org/C121955636","wikidata":"https://www.wikidata.org/wiki/Q4116214","display_name":"Accounting","level":1,"score":0.4098206162452698},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19076067209243774},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.1033291220664978},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0}],"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":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","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":"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":"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":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"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":"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":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bti617","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti617","pdf_url":null,"source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16091409","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16091409","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/15bfae04-a221-4c60-bfe9-6567ba71aee7","is_oa":false,"landing_page_url":"https://research.manchester.ac.uk/en/publications/15bfae04-a221-4c60-bfe9-6567ba71aee7","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Sanguinetti, G, Milo, M, Rattray, M & Lawrence, N D 2005, 'Accounting for probe-level noise in principal component analysis of microarray data', Bioinformatics, vol. 21, no. 19, pp. 3748-3754. https://doi.org/10.1093/bioinformatics/bti617","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5899999737739563,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1498183065","https://openalex.org/W1577436787","https://openalex.org/W2049633694","https://openalex.org/W2050354343","https://openalex.org/W2060542838","https://openalex.org/W2063339587","https://openalex.org/W2102214238","https://openalex.org/W2122598723","https://openalex.org/W2125027820","https://openalex.org/W2146004021","https://openalex.org/W2146646206","https://openalex.org/W2148541040","https://openalex.org/W2159285593","https://openalex.org/W2163988673","https://openalex.org/W2171118759","https://openalex.org/W2542444350"],"related_works":["https://openalex.org/W1975632186","https://openalex.org/W3027745756","https://openalex.org/W3205213561","https://openalex.org/W2531880140","https://openalex.org/W2126145365","https://openalex.org/W2036609560","https://openalex.org/W346861917","https://openalex.org/W3024018414","https://openalex.org/W1542592062","https://openalex.org/W4380081032"],"abstract_inverted_index":{"We":[0,21,47],"propose":[1],"a":[2,57],"new":[3,32],"model-based":[4],"approach":[5],"to":[6,26,55,61],"PCA":[7],"that":[8,77],"takes":[9],"into":[10],"account":[11],"the":[12,28,50,74,78],"variances":[13],"associated":[14],"with":[15],"each":[16,19],"gene":[17],"in":[18],"experiment.":[20],"develop":[22],"an":[23],"efficient":[24],"EM-algorithm":[25],"estimate":[27],"parameters":[29],"of":[30,73,81],"our":[31],"model.":[33],"The":[34,70],"model":[35,51,75],"provides":[36],"significantly":[37],"better":[38],"results":[39],"than":[40],"standard":[41],"PCA,":[42],"while":[43],"remaining":[44],"computationally":[45],"reasonable.":[46],"show":[48],"how":[49],"can":[52],"be":[53],"used":[54],"'denoise'":[56],"microarray":[58],"dataset":[59],"leading":[60],"improved":[62],"expression":[63],"profiles":[64],"and":[65],"tighter":[66],"clustering":[67],"across":[68],"profiles.":[69],"probabilistic":[71],"nature":[72],"means":[76],"correct":[79],"number":[80],"principal":[82],"components":[83],"is":[84],"automatically":[85],"obtained.":[86]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
