{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T02:58:35Z","timestamp":1785380315706,"version":"3.55.0"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1188,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: RNA sequencing is now widely performed to study differential expression among experimental conditions. As tests are performed on a large number of genes, stringent false-discovery rate control is required at the expense of detection power. Ad hoc filtering techniques are regularly used to moderate this correction by removing genes with low signal, with little attention paid to their impact on downstream analyses.<\/jats:p><jats:p>Results: We propose a data-driven method based on the Jaccard similarity index to calculate a filtering threshold for replicated RNA sequencing data. In comparisons with alternative data filters regularly used in practice, we demonstrate the effectiveness of our proposed method to correctly filter lowly expressed genes, leading to increased detection power for moderately to highly expressed genes. Interestingly, this data-driven threshold varies among experiments, highlighting the interest of the method proposed here.<\/jats:p><jats:p>Availability: The proposed filtering method is implemented in the R package HTSFilter available on Bioconductor.<\/jats:p><jats:p>Contact: \u00a0andrea.rau@jouy.inra.fr<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt350","type":"journal-article","created":{"date-parts":[[2013,7,3]],"date-time":"2013-07-03T04:27:49Z","timestamp":1372825669000},"page":"2146-2152","source":"Crossref","is-referenced-by-count":242,"title":["Data-based filtering for replicated high-throughput transcriptome sequencing experiments"],"prefix":"10.1093","volume":"29","author":[{"given":"Andrea","family":"Rau","sequence":"first","affiliation":[{"name":"1 INRA, UMR1313 G\u00e9n\u00e9tique animale et biologie int\u00e9grative, 78352 Jouy-en-Josas, France, 2AgroParisTech, UMR1313 G\u00e9n\u00e9tique animale et biologie int\u00e9grative, 75231 Paris 05, France and 3Inria Saclay - \u00cele-de-France, 91405 Orsay, France"},{"name":"1 INRA, UMR1313 G\u00e9n\u00e9tique animale et biologie int\u00e9grative, 78352 Jouy-en-Josas, France, 2AgroParisTech, UMR1313 G\u00e9n\u00e9tique animale et biologie int\u00e9grative, 75231 Paris 05, France and 3Inria Saclay - \u00cele-de-France, 91405 Orsay, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M\u00e9lina","family":"Gallopin","sequence":"additional","affiliation":[{"name":"1 INRA, UMR1313 G\u00e9n\u00e9tique animale et biologie int\u00e9grative, 78352 Jouy-en-Josas, France, 2AgroParisTech, UMR1313 G\u00e9n\u00e9tique animale et biologie int\u00e9grative, 75231 Paris 05, France and 3Inria Saclay - \u00cele-de-France, 91405 Orsay, France"},{"name":"1 INRA, UMR1313 G\u00e9n\u00e9tique animale et biologie int\u00e9grative, 78352 Jouy-en-Josas, France, 2AgroParisTech, UMR1313 G\u00e9n\u00e9tique animale et biologie int\u00e9grative, 75231 Paris 05, France and 3Inria Saclay - \u00cele-de-France, 91405 Orsay, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gilles","family":"Celeux","sequence":"additional","affiliation":[{"name":"1 INRA, UMR1313 G\u00e9n\u00e9tique animale et biologie int\u00e9grative, 78352 Jouy-en-Josas, France, 2AgroParisTech, UMR1313 G\u00e9n\u00e9tique animale et biologie int\u00e9grative, 75231 Paris 05, France and 3Inria Saclay - \u00cele-de-France, 91405 Orsay, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florence","family":"Jaffr\u00e9zic","sequence":"additional","affiliation":[{"name":"1 INRA, UMR1313 G\u00e9n\u00e9tique animale et biologie int\u00e9grative, 78352 Jouy-en-Josas, France, 2AgroParisTech, UMR1313 G\u00e9n\u00e9tique animale et biologie int\u00e9grative, 75231 Paris 05, France and 3Inria Saclay - \u00cele-de-France, 91405 Orsay, France"},{"name":"1 INRA, UMR1313 G\u00e9n\u00e9tique animale et biologie int\u00e9grative, 78352 Jouy-en-Josas, France, 2AgroParisTech, UMR1313 G\u00e9n\u00e9tique animale et biologie int\u00e9grative, 75231 Paris 05, France and 3Inria Saclay - \u00cele-de-France, 91405 Orsay, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,7,2]]},"reference":[{"key":"2023012810462866100_btt350-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol."},{"key":"2023012810462866100_btt350-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2202\/1544-6115.1627","article-title":"A two-stage Poisson model for testing RNA-seq data","volume":"10","author":"Auer","year":"2011","journal-title":"Stat. 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