CGHregions: dimension reduction for array CGH data with minimal information loss.
An algorithm to reduce multi-sample array CGH data from thousands of clones to tens or hundreds of clone regions is introduced. This reduction of the data is performed such that little information is lost, which is possible due to the high dependencies between neighboring clones. The algorithm is explained using a small example. The potential beneficial effects of the algorithm for downstream analysis are illustrated by re-analysis of previously published colorectal cancer data. Using multiple testing corrections suitable for these data, we provide statistical evidence for genomic differences on several clone regions between MSI+ and CIN+ tumors. The algorithm, named CGHregions, is available as an easy-to-use script in R.
van de Wiel
Mark A
MA
Department of Pathology and Department of Biostatistics (KEB), VU University Medical Center, Amsterdam, The Netherlands. mark.vdwiel@vumc.nl
Wieringen
Wessel N van
WN