Array segmentation methods.

Entries in the table indicate the proportion of times (out of 125 observations in each category) that top-down segmentation outperforms the bottom-up approach. Values smaller than (highlighted) indicate the bottom-up approach (PPC) is more appropriate than top-down (CBS) for short signals and signals with many copy-number events. Performance improves by averaging several PPC models. Note: since the PPC algorithm is stochastic, proportions can vary slightly from one run to another (variation is on the order of ).