Providing an interface between dry-bench bioinformaticians and
wet-lab biologists, DNA Methylation Microarrays: "Experimental
Design and Statistical Analysis" presents the statistical methods
and tools to analyze high-throughput epigenomic data, in
particular, DNA methylation microarray data. Since these
microarrays share the same underlying principles as gene expression
microarrays, many of the analyses in the text also apply to
microarray-based gene expression and histone modification
(ChIP-on-chip) studies.
After introducing basic statistics, the book describes wet-bench
technologies that produce the data for analysis and explains how to
preprocess the data to remove systematic artifacts resulting from
measurement imperfections. It then explores differential
methylation and genomic tiling arrays. Focusing on exploratory data
analysis, the next several chapters show how cluster and network
analyses can link the functions and roles of unannotated DNA
elements with known ones. The book concludes by surveying the open
source software (R and Bioconductor), public databases, and other
online resources available for microarray research.
Requiring only limited knowledge of statistics and programming,
this book helps readers gain a solid understanding of the
methodological foundations of DNA microarray analysis.
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