CGHcall

This site corresponds to the paper:

M.A. van de Wiel, K.I. Kim,  S.J. Vosse, W. N. van Wieringen, S.M. Wilting and B. Ylstra (2007), CGHcall: an algorithm for calling aberrations for multiple array CGH tumor profiles.  Bioinformatics, 23, 892–894.

Version 1.3.0 [Updated 15/5/09]. Bugs repaired and  inclusion of post-segmentation normalization. The latter may improve determination of the 0-level. See ?postsegnormalize]
Linux, Unix, etc [non-tested]: CGHcall.tar.gz
Windows: CGHcall.zip

Version 2.5.0 [Updated 24/6/09: is the same as version 1.4.0, but re-numbered to comply with BioConductor version ]. Faster than previous versions. Includes option for more robust calling. Includes option for more efficient file output and plotting, in particular useful for high-resolution profiles.
Linux, Unix, etc [non-tested]: CGHcall.tar.gz
Windows: CGHcall.zip

Use help(package=CGHcall) for help file. An example script for using the package.

Data set oral SCC (Snijders et al.(2005); Oncogene) is available here. (Supplementary Table B; please save as '.txt' and remove 'Target' and 'Pos' columns). BT474 and SKBR7 cell line data (Van den IJssel et al. (2005); NAR)  are available from the Gene Expression Omnibus,
via accession numbers GSM73557 and GSM75171.

Resulting plots

Oral SCC (89 plots; 9Mb)
Cervical cancer (5 plots; 1.2Mb)
Simulated data, no error on segment (50 plots; 3.2Mb)
Simulated data, additional error on segments (50 plots; 3.2Mb)


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