{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/copynumber450kcancer-baseline-correction-for","title":"CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array","arxiv_id":null,"date":"2016-04-15","proceeding":"Bioinformatics 2016 4","authors":["Nour-Al-Dain Marzouka","Jessica Nordlund","Christofer L Bäcklin","Gudmar Lönnerholm","Ann-Christine Syvänen","Jonas Carlsson Almlöf"],"abstract":"Abstract\r\nThe Illumina Infinium HumanMethylation450 BeadChip (450k) is widely used for the evaluation of DNA methylation levels in large-scale datasets, particularly in cancer. The 450k design allows copy number variant (CNV) calling using existing bioinformatics tools. However, in cancer samples, numerous large-scale aberrations cause shifting in the probe intensities and thereby may result in erroneous CNV calling. Therefore, a baseline correction process is needed. We suggest the maximum peak of probe segment density to correct the shift in the intensities in cancer samples.\r\n\r\nAvailability and implementation: CopyNumber450kCancer is implemented as an R package. The package with examples can be downloaded at http://cran.r-project.org\r\n\r\nContact: nour.marzouka@ku.ac.ae\r\n\r\nSupplementary information: Supplementary data are available at Bioinformatics online.","url_abs":"https://pubmed.ncbi.nlm.nih.gov/26553913/","url_pdf":"https://academic.oup.com/bioinformatics/article-pdf/32/7/1080/49018302/bioinformatics_32_7_1080.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"copynumber450kcancer-baseline-correction-for","repo_url":"https://github.com/NourMarzouka/CopyNumber450kCancer","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}