Rafael A. Irizarry – författare

This book presents practical approaches for the analysis of data from gene expression microarrays. Each chapter describes the conceptual and methodological underpinning for a statistical tool and its implementation in software. Methods cover all aspects of statistical analysis of microarrays, from annotation and filtering to clustering and classification. Chapters are written by the developers of the software. All software packages described are free to academic users. The book includes coverage of various packages that are part of the Bioconductor project and several related R tools. The materials presented cover a range of software tools designed for varied audiences. Some chapters describe simple menu-driven software in a user-friendly fashion, and are designed to be accessible to microarray data analysts without formal quantitative training. Most chapters are directed at microarray data analysts with master-level training in computer science, biostatistics or bioinformatics. A minority of more advanced chapters are intended for doctoral students and researchers.

Unlike the first edition, the new edition has been split into two books.Thoroughly revised and updated, this is the first book of the second edition of Introduction to Data Science: Data Wrangling and Visualization with R. It introduces skills that can help you tackle real-world data analysis challenges. These include R programming, data wrangling with dplyr, data visualization with ggplot2, file organization with UNIX/Linux shell, version control with Git and GitHub, and reproducible document preparation with Quarto and knitr. The new edition includes additional material on data.table, locales, and accessing data through APIs. The book is divided into four parts: R, Data Visualization, Data Wrangling, and Productivity Tools. Each part has several chapters meant to be presented as one lecture and includes dozens of exercises. The second book will cover topics including probability, statistics and prediction algorithms with R.Throughout the book, we use motivating case studies. In each case study, we try to realistically mimic a data scientist’s experience. For each of the skills covered, we start by asking specific questions and answer these through data analysis. Examples of the case studies included in the book are: US murder rates by state, self-reported student heights, trends in world health and economics, and the impact of vaccines on infectious disease rates.This book is meant to be a textbook for a first course in Data Science. No previous knowledge of R is necessary, although some experience with programming may be helpful. To be a successful data analyst implementing these skills covered in this book requires understanding advanced statistical concepts, such as those covered the second book. If you read and understand all the chapters and complete all the exercises in this book, and understand statistical concepts, you will be well-positioned to perform basic data analysis tasks and you will be prepared to learn the more advanced concepts and skills needed to become an expert.

Introduction to Data Science: Statistics and Prediction Algorithms Through Case Studies teaches data science as a way of thinking statistically, not just as a collection of computational tools. Building on the topics covered in Introduction to Data Science: Data Wrangling and Visualization with R, this book is designed for students with some programming experience and basic mathematical maturity, this book builds the foundations of probability, statistical inference, regression, high-dimensional data analysis, and machine learning through real data examples and reproducible R code. It is suitable for one-semester course in advanced data science.The book shows how to reason about variability, uncertainty, prediction error, model assumptions, and validation. Through case studies involving polling, genetics, baseball, recommendation systems, image classification, and other modern datasets, readers learn how to connect probability models to data, summarize complex information, quantify uncertainty, fit and interpret models, evaluate prediction algorithms, and understand the statistical ideas behind machine learning. Each chapter is designed to support classroom teaching, self-study, and hands-on analysis, with exercises and companion web materials available through the book website.Key Features:Includes base R, data.table, and tidyverse code.Focuses on the statistical and probabilistic foundations of machine learning.Contains real-world case studies.Rafael A. Irizarry is Professor and Chair of the Department of Data Science at Dana-Farber Cancer Institute and Professor of Applied Statistics at Harvard. His research focuses on Genomics and he has taught several Data Science courses.

Introduction to Data Science: Statistics and Prediction Algorithms Through Case Studies teaches data science as a way of thinking statistically, not just as a collection of computational tools. Building on the topics covered in Introduction to Data Science: Data Wrangling and Visualization with R, this book is designed for students with some programming experience and basic mathematical maturity, this book builds the foundations of probability, statistical inference, regression, high-dimensional data analysis, and machine learning through real data examples and reproducible R code. It is suitable for one-semester course in advanced data science.The book shows how to reason about variability, uncertainty, prediction error, model assumptions, and validation. Through case studies involving polling, genetics, baseball, recommendation systems, image classification, and other modern datasets, readers learn how to connect probability models to data, summarize complex information, quantify uncertainty, fit and interpret models, evaluate prediction algorithms, and understand the statistical ideas behind machine learning. Each chapter is designed to support classroom teaching, self-study, and hands-on analysis, with exercises and companion web materials available through the book website.Key Features:Includes base R, data.table, and tidyverse code.Focuses on the statistical and probabilistic foundations of machine learning.Contains real-world case studies.Rafael A. Irizarry is Professor and Chair of the Department of Data Science at Dana-Farber Cancer Institute and Professor of Applied Statistics at Harvard. His research focuses on Genomics and he has taught several Data Science courses.

This book covers several of the statistical concepts and data analytic skills needed to succeed in data-driven life science research. The authors proceed from relatively basic concepts related to computed p-values to advanced topics related to analyzing highthroughput data. They include the R code that performs this analysis and connect the lines of code to the statistical and mathematical concepts explained.

Thedevelopmentoftechnologiesforhigh–throughputmeasurementofgene expression in biological system is providing powerful new tools for inv- tigating the transcriptome on a genomic scale, and across diverse biol- ical systems and experimental designs. This technological transformation is generating an increasing demand for data analysis in biological inv- tigations of gene expression. This book focuses on data analysis of gene expression microarrays. The goal is to provide guidance to practitioners in deciding which statistical approaches and packages may be indicated for their projects, in choosing among the various options provided by those packages, and in correctly interpreting the results. The book is a collection of chapters written by authors of statistical so- ware for microarray data analysis. Each chapter describes the conceptual and methodological underpinning of data analysis tools as well as their software implementation, and will enable readers to both understand and implement an analysis approach. Methods touch on all aspects of statis- cal analysis of microarrays, from annotation and ?ltering to clustering and classi?cation. All software packages described are free to academic users. The materials presented cover a range of software tools designed for varied audiences. Some chapters describe simple menu-driven software in a user-friendly fashion and are designed to be accessible to microarray data analystswithoutformalquantitativetraining.Mostchaptersaredirectedat microarray data analysts with master’s-level training in computer science, biostatistics, or bioinformatics. A minority of more advanced chapters are intended for doctoral students and researchers.