This book covers some important methods for the analysis of micro-array data and QTL. It is also considered important that readers learn to read and understand the relevant literature, because it is a fast moving subject field. R and Bioconductor used in this book. The student can explore the dependencies and the structure in a large multivariate data set, and can apply the multivariate methods correctly. The reader can also analyze micro-arrays and he/she known the basics of QTL, linkage analysis and association studies. The reader is able to read and understand the relevant literature. Multivariate data analysis is basically a collection of many statistical methods that are applicable to large and/or high dimensional data sets. All methods that are covered in this book, are often applied in industry and research institutions.