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Article Dans Une Revue Bioinformatics Année : 2011

SMETHILLIUM: spatial normalization METHod for ILLumina InfinIUM HumanMethylation BeadChip

Résumé

Summary: DNA methylation is a major epigenetic modification in human cells. Illumina HumanMethylation27 BeadChip makes it possible to quantify the methylation state of 27 578 loci spanning 14 495 genes.We developed a non-parametric normalization method to correct the spatial background noise in order to improve the signal-to-noise ratio. The prediction performance of the proposed method was assessed on three fully methylated samples and three fully unmethylated DNA samples. We demonstrate that the spatial normalization outperforms BeadStudio to predict the methylation state of a given locus. Availability and Implementation: A R script and the data are available at the following address: http://bioinfo.curie.fr/projects/ smethillium. Contact: smethillium@curie.fr Supplementary information: Supplementary data are available at Bioinformatics online.

Dates et versions

hal-02653038 , version 1 (29-05-2020)

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Camille Sabbah, Gildas Mazo, Caroline Paccard, Fabien Reyal, Philippe Hupé. SMETHILLIUM: spatial normalization METHod for ILLumina InfinIUM HumanMethylation BeadChip. Bioinformatics, 2011, 27 (12), pp.1693-1695. ⟨10.1093/bioinformatics/btr187⟩. ⟨hal-02653038⟩
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