ArticleFrontiers in genetics2015
Between-array normalization for 450K data.
Article in Frontiers in genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Epigenome-wide DNA methylation in leukocytes and toenail metals: The normative aging study.Environmental research · 2023Article
- Improving Infinium MethylationEPIC data processing: re-annotation of enhancers and long noncoding RNA genes and benchmarking of normalization methods.Epigenetics · 2022Article
- Updates to data versions and analytic methods influence the reproducibility of results from epigenome-wide association studies.Epigenetics · 2022Article
- DNA methylation profiles unique to Kalahari KhoeSan individuals.Epigenetics · 2021Article
- Meffil: efficient normalization and analysis of very large DNA methylation datasets.Bioinformatics (Oxford, England) · 2018Article
- Methods for CpG Methylation Array Profiling Via Bisulfite Conversion.Methods in molecular biology (Clifton, N.J.) · 2018Review
- Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children's Environmental Health Studies: The Children's Environmental Health and Disease Prevention Research Center's Epigenetics Working Group.Environmental health perspectives · 2017Article
- Epigenome-wide discovery and evaluation of leukocyte DNA methylation markers for the detection of colorectal cancer in a screening setting.Clinical epigenetics · 2017Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Illumina Infinium HumanMethylation450 BeadChip is frequently used in epigenetic research. Besides quantile normalization there is currently no standard method to normalize the data between arrays. We describe some properties of the data generated by this platform and present a normalization method based on local regression. We compare the performance of this method with other commonly used approaches in three benchmarks (correlation between 21 pairs of technical replicates, detection of differential methylation and correlation of methylation levels for smoking-associated CpG sites with smoking behavior of 655 participants of an epidemiological study). Results indicate that the proposed method improves reproducibility, whereas some commonly used methods can have adverse effects.
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