Brief Introduction into Using R
To get started a gentle introduction to the statistical programming language R will be given (R Development Core Team, 2009), specific for our purposes. This will solve the practical issues to follow the stream of reasoning. In particular, it is briefly explained how to install R and Bioconductor, how to obtain help, and how to perform simple calculations. Since many computations are essentially performed on data vectors, several basic illustrations of this are given. With respect to gene expressions the data vectors are placed one beneath the other to form a data matrix with the genes as rows and the patients as columns. The idea of a data matrix is extensively explained and illustrated by several examples. A larger example consists of the classical Golub et al. (1999) data, which will be analyzed frequently to illustrate statistical procedures.