Chapter title |
A Guide to Illumina BeadChip Data Analysis
|
---|---|
Chapter number | 16 |
Book title |
DNA Methylation Protocols
|
Published in |
Methods in molecular biology, January 2018
|
DOI | 10.1007/978-1-4939-7481-8_16 |
Pubmed ID | |
Book ISBNs |
978-1-4939-7479-5, 978-1-4939-7481-8
|
Authors |
Michael C. Wu, Pei-Fen Kuan |
Abstract |
The Illumina Infinium BeadChips are a powerful array-based platform for genome-wide DNA methylation profiling at approximately 485,000 (450K) and 850,000 (EPIC) CpG sites across the genome. The platform is used in many large-scale population-based epigenetic studies of complex diseases, environmental exposures, or other experimental conditions. This chapter provides an overview of the key steps in analyzing Illumina BeadChip data. We describe key preprocessing steps including data extraction and quality control as well as normalization strategies. We further present principles and guidelines for conducting association analysis at the individual CpG level as well as more sophisticated pathway-based association tests. |
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Unknown | 1 | 100% |
Demographic breakdown
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Members of the public | 1 | 100% |
Mendeley readers
Geographical breakdown
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Unknown | 69 | 100% |
Demographic breakdown
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Student > Ph. D. Student | 16 | 23% |
Researcher | 11 | 16% |
Student > Bachelor | 8 | 12% |
Student > Master | 8 | 12% |
Student > Doctoral Student | 3 | 4% |
Other | 6 | 9% |
Unknown | 17 | 25% |
Readers by discipline | Count | As % |
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Medicine and Dentistry | 5 | 7% |
Agricultural and Biological Sciences | 4 | 6% |
Engineering | 4 | 6% |
Nursing and Health Professions | 2 | 3% |
Other | 10 | 14% |
Unknown | 21 | 30% |