A data-driven approach to preprocessing Illumina 450K methylation array data
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...For the methylation data (Illumina Infinium 450k arrays), the median absolute deviation was employed to select the top 4000 most variable CpG sites after beta-mixture quantile normalization (Pidsley et al., 2013)....
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..., 2013], dasen [Pidsley et al., 2013], and noob [Triche et al....
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...Supplementary Figures S3a,b contains results for additional preprocessing methods: BMIQ [Teschendorff et al., 2013], SWAN [Maksimovic et al., 2012] and dasen [Pidsley et al., 2013]....
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...Funnorm improves X and Y chromosomes probes prediction in blood samples As suggested previously [Pidsley et al., 2013], one can benchmark performance by identifying DMPs associated with sex....
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...Funnorm improves X and Y chromosomes probes prediction in blood samples As suggested previously [Pidsley et al., 2013], one can benchmark performance by identifying DMPs associated with sex....
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...Several methods have been proposed for normalization of the 450k array, including Quantile normalization [Touleimat and Tost, 2012, Aryee et al., 2014], SWAN [Maksimovic et al., 2012], BMIQ [Teschendorff et al., 2013], dasen [Pidsley et al., 2013], and noob [Triche et al., 2013]....
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...Standard, specially constructed control datasets produced by spiking samples have been influential in the gene expression field [13], but would not be as suitable for analysis of DNA methylation....
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...Quantile normalization (QN) is a well established technique in gene expression analysis, where it has been shown to perform well [13]....
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