{"id":"https://openalex.org/W2100371358","doi":"https://doi.org/10.1093/bioinformatics/bts629","title":"AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data","display_name":"AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data","publication_year":2012,"publication_date":"2012-10-24","ids":{"openalex":"https://openalex.org/W2100371358","doi":"https://doi.org/10.1093/bioinformatics/bts629","mag":"2100371358","pmid":"https://pubmed.ncbi.nlm.nih.gov/23097420"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts629","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts629","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/129/49060334/bioinformatics_29_1_129.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/129/49060334/bioinformatics_29_1_129.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004907038","display_name":"Mario Fasold","orcid":"https://orcid.org/0000-0001-8299-4149"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Mario Fasold","raw_affiliation_strings":["1 Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, D-4107 Leipzig, Haertelstr. 16-18, Germany and 2Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, D-4107 Leipzig, Haertelstr. 16-18, Germany and 2Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045754538","display_name":"Hans Binder","orcid":"https://orcid.org/0000-0002-2242-4678"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Hans Binder","raw_affiliation_strings":["1 Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, D-4107 Leipzig, Haertelstr. 16-18, Germany and 2Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, D-4107 Leipzig, Haertelstr. 16-18, Germany and 2Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5004907038"],"corresponding_institution_ids":["https://openalex.org/I926574661"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":0.3742,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.60156808,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":97},"biblio":{"volume":"29","issue":"1","first_page":"129","last_page":"131"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.6272000074386597,"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":0.6272000074386597,"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/T12610","display_name":"RNA regulation and disease","score":0.04859999939799309,"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/bioconductor","display_name":"Bioconductor","score":0.989264726638794},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5763240456581116},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5406534075737},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.46714919805526733},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4645886719226837},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.45256027579307556},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43289926648139954},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.41693341732025146},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4109402596950531},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41055986285209656},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25496357679367065},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.246925950050354},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1432599127292633},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.13945704698562622},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.08839479088783264}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.989264726638794},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5763240456581116},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5406534075737},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.46714919805526733},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4645886719226837},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.45256027579307556},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43289926648139954},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.41693341732025146},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4109402596950531},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41055986285209656},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25496357679367065},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.246925950050354},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1432599127292633},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.13945704698562622},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.08839479088783264},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[{"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":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000592","qualifier_name":"standards","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":"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":"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":"D020871","descriptor_name":"RNA Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020871","descriptor_name":"RNA Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020871","descriptor_name":"RNA Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts629","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts629","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/129/49060334/bioinformatics_29_1_129.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23097420","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23097420","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:2527658","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3530908","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.879.8086","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.879.8086","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2012/10/24/bioinformatics.bts629.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts629","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts629","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/129/49060334/bioinformatics_29_1_129.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320328735","display_name":"Freistaat Sachsen","ror":null},{"id":"https://openalex.org/F4320338080","display_name":"European Social Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2100371358.pdf","grobid_xml":"https://content.openalex.org/works/W2100371358.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1696199194","https://openalex.org/W2078068395","https://openalex.org/W2100008799","https://openalex.org/W2116634113","https://openalex.org/W2148512171","https://openalex.org/W2154273881","https://openalex.org/W2164331322","https://openalex.org/W2167907413"],"related_works":["https://openalex.org/W2366720351","https://openalex.org/W2113065873","https://openalex.org/W2512452276","https://openalex.org/W2923101443","https://openalex.org/W2767491792","https://openalex.org/W2112504441","https://openalex.org/W2131192238","https://openalex.org/W2580435991","https://openalex.org/W2268267797","https://openalex.org/W2105642898"],"abstract_inverted_index":{"MOTIVATION:":[0],"Gene":[1],"expression":[2,39],"experiments":[3],"aim":[4],"to":[5,15,54,58,67],"accurately":[6],"quantify":[7],"thousands":[8],"of":[9,31,45],"transcripts":[10],"in":[11,28,63,87],"parallel.":[12],"Factors":[13],"posterior":[14],"RNA":[16,24,61],"extraction":[17],"can,":[18],"however,":[19],"impair":[20],"their":[21],"accurate":[22],"representation.":[23],"degradation":[25,73],"and":[26,66],"differences":[27],"the":[29,50,60,72,88,102],"efficiency":[30],"amplification":[32],"affect":[33],"raw":[34],"intensity":[35,43],"measurements":[36],"using":[37],"Affymetrix":[38],"arrays.":[40],"The":[41,95],"positional":[42],"decay":[44],"specifically":[46],"hybridized":[47],"probes":[48],"along":[49],"transcript":[51],"they":[52],"intend":[53],"interrogate":[55],"is":[56,83,85,97],"used":[57],"estimate":[59],"quality":[62],"a":[64],"sample":[65],"correct":[68],"probe":[69],"intensities":[70],"for":[71,77],"bias.":[74],"This":[75],"functionality,":[76],"which":[78],"no":[79],"previous":[80],"software":[81],"solution":[82],"available,":[84],"implemented":[86],"R/Bioconductor":[89],"package":[90,96],"AffyRNADegradation":[91],"presented":[92],"here.":[93],"AVAILABILITY:":[94],"available":[98],"via":[99],"Bioconductor":[100],"at":[101],"URL":[103],"http://bioconductor.org/packages/release/bioc/html/AffyRNA":[104],"Degradation.html":[105]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
