After data preprocessing and cross-platform matching (as described in Cope, L., Zhong, X., Garrett-Mayer, E., Parmigiani, G. and Gabrielson, E.: Cross-study validation of a molecular profile for BRCA1-linked breast cancers, working paper), we obtain a combined dataset with 1658 features and 118 samples. Here, BRCA1 is linked to breast cancer.