Sandrine Dudoit - Böcker

Bioconductor is a widely used open source and open development software project for the analysis and comprehension of data arising from high-throughput experimentation in genomics and molecular biology. Bioconductor is rooted in the open source statistical computing environment R. This volume's coverage is broad and ranges across most of the key capabilities of the Bioconductor project, including importation and preprocessing of high-throughput data from microarray, proteomic, and flow cytometry platforms:Curation and delivery of biological metadata for use in statistical modeling and interpretationStatistical analysis of high-throughput data, including machine learning and visualizationModeling and visualization of graphs and networksThe developers of the software, who are in many cases leading academic researchers, jointly authored chapters. All methods are illustrated with publicly available data, and a major section of the book is devoted to exposition of fully worked case studies. This book is more than a static collection of descriptive text, figures, and code examples that were run by the authors to produce the text; it is a dynamic document.Code underlying all of the computations that are shown is made available on a companion website, and readers can reproduce every number, figure, and table on their own computers.

This book establishes the theoretical foundations of a general methodology for multiple hypothesis testing and discusses its software implementation in R and SAS. These are applied to a range of problems in biomedical and genomic research, including identification of differentially expressed and co-expressed genes in high-throughput gene expression experiments; tests of association between gene expression measures and biological annotation metadata; sequence analysis; and genetic mapping of complex traits using single nucleotide polymorphisms. The procedures are based on a test statistics joint null distribution and provide Type I error control in testing problems involving general data generating distributions, null hypotheses, and test statistics.

This book establishes the theoretical foundations of a general methodology for multiple hypothesis testing and discusses its software implementation in R and SAS. These are applied to a range of problems in biomedical and genomic research, including identification of differentially expressed and co-expressed genes in high-throughput gene expression experiments; tests of association between gene expression measures and biological annotation metadata; sequence analysis; and genetic mapping of complex traits using single nucleotide polymorphisms. The procedures are based on a test statistics joint null distribution and provide Type I error control in testing problems involving general data generating distributions, null hypotheses, and test statistics.

The purpose of this volume is to provide an overview of Terry Speed’s contributions to statistics and beyond. Each of the fifteen chapters concerns a particular area of research and consists of a commentary by a subject-matter expert and selection of representative papers. The chapters, organized more or less chronologically in terms of Terry’s career, encompass a wide variety of mathematical and statistical domains, along with their application to biology and medicine. Accordingly, earlier chapters tend to be more theoretical, covering some algebra and probability theory, while later chapters concern more recent work in genetics and genomics. The chapters also span continents and generations, as they present research done over four decades, while crisscrossing the globe.The commentaries provide insight into Terry’s contributions to a particular area of research, by summarizing his work and describing its historical and scientific context, motivation, and impact. In addition to shedding light on Terry’s scientific achievements, the commentaries reveal endearing aspects of his personality, such as his intellectual curiosity, energy, humor, and generosity.