{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,21]],"date-time":"2026-06-21T11:04:52Z","timestamp":1782039892370,"version":"3.54.5"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Heterogeneity and latent variables are now widely recognized as major sources of bias and variability in high-throughput experiments. The most well-known source of latent variation in genomic experiments are batch effects\u2014when samples are processed on different days, in different groups or by different people. However, there are also a large number of other variables that may have a major impact on high-throughput measurements. Here we describe the sva package for identifying, estimating and removing unwanted sources of variation in high-throughput experiments. The sva package supports surrogate variable estimation with the sva function, direct adjustment for known batch effects with the ComBat function and adjustment for batch and latent variables in prediction problems with the fsva function.<\/jats:p>\n               <jats:p>Availability: The R package sva is freely available from http:\/\/www.bioconductor.org.<\/jats:p>\n               <jats:p>Contact: \u00a0jleek@jhsph.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts034","type":"journal-article","created":{"date-parts":[[2012,1,19]],"date-time":"2012-01-19T01:59:28Z","timestamp":1326938368000},"page":"882-883","source":"Crossref","is-referenced-by-count":5638,"title":["The <tt>sva<\/tt> package for removing batch effects and other unwanted variation in high-throughput experiments"],"prefix":"10.1093","volume":"28","author":[{"given":"Jeffrey T.","family":"Leek","sequence":"first","affiliation":[{"name":"1 Department of Biostatistics, JHU Bloomberg School of Public Health, Baltimore, MD, 2Division of Computational Biomedicine, Boston University, Boston, MA, 3Department of Epidemiology, JHU Bloomberg School of Public Health, Baltimore, MD and 4Lewis-Sigler Institute, Department of Molecular Biology, Princeton University, Princeton, NJ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"W. Evan","family":"Johnson","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, JHU Bloomberg School of Public Health, Baltimore, MD, 2Division of Computational Biomedicine, Boston University, Boston, MA, 3Department of Epidemiology, JHU Bloomberg School of Public Health, Baltimore, MD and 4Lewis-Sigler Institute, Department of Molecular Biology, Princeton University, Princeton, NJ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hilary S.","family":"Parker","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, JHU Bloomberg School of Public Health, Baltimore, MD, 2Division of Computational Biomedicine, Boston University, Boston, MA, 3Department of Epidemiology, JHU Bloomberg School of Public Health, Baltimore, MD and 4Lewis-Sigler Institute, Department of Molecular Biology, Princeton University, Princeton, NJ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew E.","family":"Jaffe","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, JHU Bloomberg School of Public Health, Baltimore, MD, 2Division of Computational Biomedicine, Boston University, Boston, MA, 3Department of Epidemiology, JHU Bloomberg School of Public Health, Baltimore, MD and 4Lewis-Sigler Institute, Department of Molecular Biology, Princeton University, Princeton, NJ, USA"},{"name":"1 Department of Biostatistics, JHU Bloomberg School of Public Health, Baltimore, MD, 2Division of Computational Biomedicine, Boston University, Boston, MA, 3Department of Epidemiology, JHU Bloomberg School of Public Health, Baltimore, MD and 4Lewis-Sigler Institute, Department of Molecular Biology, Princeton University, Princeton, NJ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John D.","family":"Storey","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, JHU Bloomberg School of Public Health, Baltimore, MD, 2Division of Computational Biomedicine, Boston University, Boston, MA, 3Department of Epidemiology, JHU Bloomberg School of Public Health, Baltimore, MD and 4Lewis-Sigler Institute, Department of Molecular Biology, Princeton University, Princeton, NJ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2012,1,17]]},"reference":[{"key":"2023012512202418500_B1","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1126\/science.1069516","article-title":"Genetic dissection of transcriptional regulation in budding yeast","volume":"296","author":"Brem","year":"2002","journal-title":"Science"},{"key":"2023012512202418500_B2","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/nrg2383","article-title":"The environmental contribution to gene expression profiles","volume":"9","author":"Gibson","year":"2008","journal-title":"Nat. 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Biol."},{"key":"2023012512202418500_B10","doi-asserted-by":"crossref","first-page":"1496","DOI":"10.1093\/bioinformatics\/btr171","article-title":"Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies","volume":"27","author":"Teschendorff","year":"2011","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/6\/882\/48880603\/bioinformatics_28_6_882.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/6\/882\/48880603\/bioinformatics_28_6_882.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:38:28Z","timestamp":1674661108000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/6\/882\/311263"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,1,17]]},"references-count":10,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2012,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts034","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,3,15]]},"published":{"date-parts":[[2012,1,17]]}}}