{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T20:45:24Z","timestamp":1783457124340,"version":"3.55.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The Illumina HumanMethylation450 BeadChip has been extensively utilized in epigenome-wide association studies. This array and its successor, the MethylationEPIC array, use two types of probes\u2014Infinium I (type I) and Infinium II (type II)\u2014in order to increase genome coverage but differences in probe chemistries result in different type I and II distributions of methylation values. Ignoring the difference in distributions between the two probe types may bias downstream analysis.<\/jats:p>\n               <jats:p>Results: Here, we developed a novel method, called Regression on Correlated Probes (RCP), which uses the existing correlation between pairs of nearby type I and II probes to adjust the beta values of all type II probes. We evaluate the effect of this adjustment on reducing probe design type bias, reducing technical variation in duplicate samples, improving accuracy of measurements against known standards, and retention of biological signal. We find that RCP is statistically significantly better than unadjusted data or adjustment with alternative methods including SWAN and BMIQ.<\/jats:p>\n               <jats:p>Availability: We incorporated the method into the R package ENmix , which is freely available from the Bioconductor website ( https:\/\/www.bioconductor.org\/packages\/release\/bioc\/html\/ENmix.html ).<\/jats:p>\n               <jats:p>Contact: \u00a0niulg@ucmail.uc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw285","type":"journal-article","created":{"date-parts":[[2016,5,6]],"date-time":"2016-05-06T03:04:47Z","timestamp":1462503887000},"page":"2659-2663","source":"Crossref","is-referenced-by-count":149,"title":["RCP: a novel probe design bias correction method for Illumina Methylation BeadChip"],"prefix":"10.1093","volume":"32","author":[{"given":"Liang","family":"Niu","sequence":"first","affiliation":[{"name":"1 Division of Biostatistics and Bioinformatics, Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zongli","family":"Xu","sequence":"additional","affiliation":[{"name":"2 Epidemiology Branch"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jack A.","family":"Taylor","sequence":"additional","affiliation":[{"name":"2 Epidemiology Branch"},{"name":"3 Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,5,5]]},"reference":[{"key":"2023020112590103400_btw285-B1","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1016\/j.ygeno.2011.07.007","article-title":"High density DNA methylation array with single CpG site resolution","volume":"98","author":"Bibikova","year":"2011","journal-title":"Genomics"},{"key":"2023020112590103400_btw285-B2","doi-asserted-by":"crossref","first-page":"771","DOI":"10.2217\/epi.11.105","article-title":"Evaluation of the Infinium Methylation 450K technology","volume":"3","author":"Dedeurwaerder","year":"2011","journal-title":"Epigenomics"},{"key":"2023020112590103400_btw285-B3","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1038\/ng1909","article-title":"DNA methylation profiling of human chromosomes 6, 20 and 22","volume":"38","author":"Eckhardt","year":"2006","journal-title":"Nat. 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Cancer Inst"},{"key":"2023020112590103400_btw285-B10","doi-asserted-by":"crossref","first-page":"e20","DOI":"10.1093\/nar\/gkv907","article-title":"ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip","volume":"44","author":"Xu","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020112590103400_btw285-B11","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/s13059-015-0581-9","article-title":"Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements","volume":"16","author":"Zhang","year":"2015","journal-title":"Genome Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/17\/2659\/49021497\/bioinformatics_32_17_2659.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/17\/2659\/49021497\/bioinformatics_32_17_2659.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:58:56Z","timestamp":1675292336000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/17\/2659\/2450739"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,5,5]]},"references-count":11,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2016,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw285","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,9,1]]},"published":{"date-parts":[[2016,5,5]]}}}