This book provides a practical guide to analysis of simple and complex method comparison data, using Stata, SAS and R. It takes the classical Limits of Agreement as a starting point, and presents it in a proper statistical framework. The model serves as a reference for reporting sources of variation and for providing conversion equations and plots between methods for practical use, including prediction uncertainty. Presents a modeling framework for analysis of data and reporting of results from comparing measurements from different clinical centers and/or different methods. Provides the practical tools for analyzing method comparison studies along with guidance on what to report and how to plan comparison studies and advice on appropriate software. Illustrated throughout with computer examples in R. Supported by a supplementary website hosting an R-package that performs the major part of the analyses needed in the area. Examples in SAS and Stata for the most common situations are also provided. Written by an acknowledged expert on the subject, with a long standing experience as a biostatistician in a clinical environment and a track record of delivering training on the subject. Biostatisticians, clinicians, medical researchers and practitioners involved in research and analysis of measurement methods and laboratory investigations will benefit from this book. Students of statistics, biostatistics, and the chemical sciences will also find this book useful.