The aim of these analysis notes is to give a basic introduction to PAM50 intrinsic subtypes and risk of reccurence score (Parker09JCO, PMID 19204204) using a published breast cancer dataset. These notes are generated using an R code bundle available at github.com/lovrot/misc-examples-pam50, and the aim of this bundle is also to show how one can use the ProjectTemplate framework for a data analysis project.