The DOI matches its Crossref record; 35 of the 35 references it cites were found in a registry or an index.
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi
Open accessAbstract
Summary: The minfi package is widely used for analyzing Illumina DNA methylation array data. Here we describe modifications to the minfi package required to support the HumanMethylationEPIC (‘EPIC’) array from Illumina. We discuss methods for the joint analysis and normalization of data from the HumanMethylation450 (‘450k’) and EPIC platforms. We introduce the single-sample Noob (ssNoob) method, a normalization procedure suitable for incremental preprocessing of individual methylation arrays and conclude that this method should be used when integrating data from multiple generations of Infinium methylation arrays. We show how to use reference 450k datasets to estimate cell type composition of samples on EPIC arrays. The cumulative effect of these updates is to ensure that minfi provides the tools to best integrate existing and forthcoming Illumina methylation array data. Availability and Implementation: The minfi package version 1.19.12 or higher is available for all platforms from the Bioconductor project. Supplementary information: Supplementary data are available at Bioinformatics online.
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Bioconductor: open software development for computational biology and bioinformatics
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Self-citationOrchestrating high-throughput genomic analysis with Bioconductor
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Self-citationComprehensive molecular characterization of clear cell renal cell carcinoma
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DNA methylation arrays as surrogate measures of cell mixture distribution
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DNA methylation GrimAge strongly predicts lifespan and healthspan
Lu, A. T., Quach, A., Wilson, J. G., Reiner, A. P., Aviv, A., Raj, K., Hou, L., Baccarelli, A. A., Li, Y., Stewart, J. D., et al. (2019) · Aging · doi:10.18632/aging.101684 · Cited by 2,540
Harmonization of multi-site diffusion tensor imaging data
Fortin, J.-P., Parker, D., Tunç, B., Watanabe, T., Elliott, M. A., Ruparel, K., Roalf, D. R., Satterthwaite, T. D., Gur, R. C., Gur, R. E., et al. (2017) · NeuroImage · doi:10.1016/j.neuroimage.2017.08.047 · Cited by 1,261
Self-citationReprogramming to recover youthful epigenetic information and restore vision
Lu, Y., Brommer, B., Tian, X., Krishnan, A., Meer, M., Wang, C., Vera, D. L., Zeng, Q., Yu, D., Bonkowski, M. S., et al. (2020) · Nature · doi:10.1038/s41586-020-2975-4 · Cited by 820
““Noob” normalization was implemented using the “minfi” R package 55,56 .”
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma
Clark, D. J., Dhanasekaran, S. M., Petralia, F., Pan, J., Song, X., Hu, Y., da Veiga Leprevost, F., Reva, B., Lih, T.-S. M., Chang, H.-Y., et al. (2019) · Cell · doi:10.1016/j.cell.2019.10.007 · Cited by 730
SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions
Zhou, W., Triche, T. J., Laird, P. W., & Shen, H. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky691 · Cited by 521
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Metadata
- Authors
- Fortin, J.-P., Triche, T. J., & Hansen, K. D.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-11-29
- Volume
- 33
- Issue
- 4
- Pages
- 558-560
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2567721002
- Cited by
- 865
- References
- 35
- FWCI
- 15.65
- Type
- journal article
- Language
- en
- Open access
- hybrid
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