{"id":"https://openalex.org/W2511704020","doi":"https://doi.org/10.1093/bib/bbx008","title":"Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions","display_name":"Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions","publication_year":2017,"publication_date":"2017-01-30","ids":{"openalex":"https://openalex.org/W2511704020","doi":"https://doi.org/10.1093/bib/bbx008","mag":"2511704020","pmid":"https://pubmed.ncbi.nlm.nih.gov/28334202"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbx008","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbx008","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1609.00959","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066730876","display_name":"Ciaran Evans","orcid":"https://orcid.org/0000-0003-3256-011X"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ciaran Evans","raw_affiliation_strings":["Department of Statistics, Baker Hall, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Baker Hall, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012301555","display_name":"Johanna Hardin","orcid":"https://orcid.org/0000-0001-6251-1955"},"institutions":[{"id":"https://openalex.org/I177881444","display_name":"Pomona College","ror":"https://ror.org/0074grg94","country_code":"US","type":"education","lineage":["https://openalex.org/I177881444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Johanna Hardin","raw_affiliation_strings":["Pomona College"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pomona College","institution_ids":["https://openalex.org/I177881444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048488682","display_name":"Daniel M. Stoebel","orcid":"https://orcid.org/0000-0002-9461-7567"},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel M Stoebel","raw_affiliation_strings":["Harvey Mudd College","Harvey Mudd Coll"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Harvey Mudd College","institution_ids":["https://openalex.org/I133543626"]},{"raw_affiliation_string":"Harvey Mudd Coll","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5066730876"],"corresponding_institution_ids":["https://openalex.org/I74973139"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.2234,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.77997762,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"19","issue":"5","first_page":"776","last_page":"792"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9991000294685364,"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/T10604","display_name":"RNA Research and Splicing","score":0.9965000152587891,"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":0.9146565794944763},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5780383348464966},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.5604591369628906},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.550321102142334},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4559491276741028},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39898261427879333},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33982527256011963}],"concepts":[{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.9146565794944763},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5780383348464966},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.5604591369628906},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.550321102142334},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4559491276741028},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39898261427879333},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33982527256011963},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"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/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"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":"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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","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":"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":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/bib/bbx008","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbx008","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28334202","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28334202","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:arXiv.org:1609.00959","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1609.00959","pdf_url":"https://arxiv.org/pdf/1609.00959","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},{"id":"mag:2511704020","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1609.00959.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"pmh:oai:europepmc.org:5124908","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6171491","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:6171491","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6171491","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":"Brief Bioinform","raw_type":"Text"},{"id":"doi:10.48550/arxiv.1609.00959","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1609.00959","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1609.00959","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1609.00959","pdf_url":"https://arxiv.org/pdf/1609.00959","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1986957831","display_name":null,"funder_award_id":"52007555","funder_id":"https://openalex.org/F4320316866","funder_display_name":"Pomona College"},{"id":"https://openalex.org/G5111189878","display_name":null,"funder_award_id":"52007544","funder_id":"https://openalex.org/F4320306082","funder_display_name":"Howard Hughes Medical Institute"},{"id":"https://openalex.org/G6198758400","display_name":null,"funder_award_id":"52007555","funder_id":"https://openalex.org/F4320306082","funder_display_name":"Howard Hughes Medical Institute"},{"id":"https://openalex.org/G8745301779","display_name":null,"funder_award_id":"52007544","funder_id":"https://openalex.org/F4320309332","funder_display_name":"Harvey Mudd College"}],"funders":[{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320309332","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45"},{"id":"https://openalex.org/F4320316866","display_name":"Pomona College","ror":"https://ror.org/0074grg94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1500600592","https://openalex.org/W1569946922","https://openalex.org/W1981509058","https://openalex.org/W1983064113","https://openalex.org/W1983253191","https://openalex.org/W1992507121","https://openalex.org/W2009458183","https://openalex.org/W2039521726","https://openalex.org/W2055027171","https://openalex.org/W2061537056","https://openalex.org/W2064397275","https://openalex.org/W2066502238","https://openalex.org/W2070494252","https://openalex.org/W2072532688","https://openalex.org/W2107018762","https://openalex.org/W2110065044","https://openalex.org/W2114104545","https://openalex.org/W2114504176","https://openalex.org/W2120865735","https://openalex.org/W2125905177","https://openalex.org/W2128942010","https://openalex.org/W2129271620","https://openalex.org/W2129633222","https://openalex.org/W2135598172","https://openalex.org/W2137526110","https://openalex.org/W2141458291","https://openalex.org/W2142165994","https://openalex.org/W2147109452","https://openalex.org/W2152239989","https://openalex.org/W2154431984","https://openalex.org/W2156631105","https://openalex.org/W2161577298","https://openalex.org/W2165909549","https://openalex.org/W2166820820","https://openalex.org/W2167869412","https://openalex.org/W2168342464","https://openalex.org/W2169001731","https://openalex.org/W2174612238","https://openalex.org/W2179438025","https://openalex.org/W2201642794","https://openalex.org/W2226446765"],"related_works":["https://openalex.org/W2559379736","https://openalex.org/W2178350464","https://openalex.org/W2884005840","https://openalex.org/W3198874062","https://openalex.org/W2137856365","https://openalex.org/W2177183743","https://openalex.org/W2051219652","https://openalex.org/W2610784813","https://openalex.org/W2997922612","https://openalex.org/W2952689055","https://openalex.org/W2404009650","https://openalex.org/W2949690567","https://openalex.org/W2611056508","https://openalex.org/W2347048027","https://openalex.org/W2231747867","https://openalex.org/W2320596164","https://openalex.org/W3012119999","https://openalex.org/W2917558237","https://openalex.org/W2097392849","https://openalex.org/W2954743601"],"abstract_inverted_index":{"RNA-Seq":[0,21,105],"is":[1,23,67,130],"a":[2,47,84,164,170,181],"widely":[3],"used":[4],"method":[5,172],"for":[6,33,132,136,186],"studying":[7],"the":[8,68,72,77,88,91,101,119,137,187],"behavior":[9],"of":[10,39,65,79,90,111,121,127,184],"genes":[11],"under":[12],"different":[13],"biological":[14,165],"conditions.":[15],"An":[16,62],"essential":[17],"step":[18],"in":[19,25,43,58,159],"an":[20,125],"study":[22],"normalization,":[24],"which":[26,71],"raw":[27,104],"data":[28,138],"are":[29,152,176],"adjusted":[30],"to":[31],"account":[32],"factors":[34],"that":[35,175,179],"prevent":[36],"direct":[37],"comparison":[38],"expression":[40,60,185],"measures.":[41],"Errors":[42],"normalization":[44,66,116,145,171],"can":[45,82],"have":[46,83],"significant":[48],"impact":[49,86],"on":[50,70,87],"downstream":[51],"analysis,":[52],"such":[53],"as":[54,124],"inflated":[55],"false":[56],"positives":[57],"differential":[59],"analysis.":[61,161],"underemphasized":[63],"feature":[64],"assumptions":[69,81,99,129,151,174],"methods":[73,117,134,146],"rely":[74],"and":[75,108,154,178],"how":[76,98,155],"validity":[78],"these":[80],"substantial":[85],"performance":[89],"methods.":[92],"In":[93],"this":[94,156],"article,":[95],"we":[96,142],"explain":[97],"provide":[100],"link":[102],"between":[103],"read":[106],"counts":[107],"meaningful":[109,182],"measures":[110],"gene":[112],"expression.":[113],"We":[114],"examine":[115],"from":[118],"perspective":[120],"their":[122,150],"assumptions,":[123],"understanding":[126],"methodological":[128],"necessary":[131],"choosing":[133],"appropriate":[135],"at":[139],"hand.":[140],"Furthermore,":[141],"discuss":[143],"why":[144],"perform":[147],"poorly":[148],"when":[149],"violated":[153],"causes":[157],"problems":[158],"subsequent":[160],"To":[162],"analyze":[163],"experiment,":[166],"researchers":[167],"must":[168],"select":[169],"with":[173],"met":[177],"produces":[180],"measure":[183],"given":[188],"experiment.":[189]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-01T08:55:40.977307","created_date":"2025-10-10T00:00:00"}
