CGHregions

This site corresponds to the paper:

CGHregions: dimension reduction for array CGH data with minimal information loss by
Mark A. van de Wiel and Wessel N. van Wieringen, 2007, Cancer Informatics, 2, 55-63.

The R-scripts, including manual: CGHregions2.3.zip (updated Aug 24 2007: repaired some bugs)
Some plotting functionality for the regions may be found in this R-script: CGHRegionsPlot.R
Example data, called array CGH data: Douglas2004CancersCALLS.txt
Original data are available here. (Douglas et al. , 2004; Cancer Res. 64, 4817-4825)

NOTE: THE R-SCRIPTS ARE NOT MAINTAINED. INSTEAD USE THE R-PACKAGE [updated 21/07/2010]:
CGHregions_1.7.1.zip (for Unix/Linux: CGHregions_1.7.1.tar.gz)
The R-package operates on CGHcall data.  The R-package CGHbase_1.2.0.zip (by Sjoerd Vosse)  manages the CGH data types (for Unix/Linux: CGHbase_1.2.0.tar.gz).

Example script for using the CGHregions package.

Additional software for (CGH) micro-array analysis is available from the VUmc microarray core facility.