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. Suitable for R versions < 2.10.0.
Linux, Unix, etc [non-tested]: CGHcall.tar.gz
Windows: CGHcall.zip

Version 2.8.0 Same as 2.5.0 but suitable for R versions >= 2.10.0.
Linux, Unix, etc [non-tested]: CGHcall.tar.gz
Windows: CGHcall.zip

Version 2.9.1 New, more memory-efficient version. Same functionality as previous, but CGHcall function is split into two functions:
CGHcall and ExpandCGHcall. The latter unpacks the result from CGHcall into a CGHcall object.
Linux, Unix, etc [non-tested]: CGHcall.tar.gz
Windows: CGHcall.zip

Version 2.9.3  Update of 2.9.1: also reports parameter values of the fitted mixture model.
Linux, Unix, etc [non-tested]: CGHcall.tar.gz
Windows: CGHcall.zip

Version 2.17.0 [Note, the jump in version number is due to BioConductor]  Update of 2.9.3: Faster, allows for parallel computing, cellularity correction included in calling step instead of in normalization,
segmentation: allows differential undo.SD [DNAcopy option] for long and short segments,  allows 5-state calling (including double deletion). Plotting (thanks: Ilari Scheinin): bugs repaired, spacing represents genomic spacing, double deletions are shown as tick marks, MAD [robust sd estimate] values added
Linux, Unix, etc [non-tested]: CGHcall.tar.gz
Windows: CGHcall.zip

Version 2.17.2 Bugs from 2.17.0 repaired. Inconsistencies with CGHbase resolved. Please re-install CGHbase as well!
These versions are submitted to BioC
Linux, Unix, etc [non-tested]: CGHcall.tar.gz ; CGHbase.tar.gz
Windows: CGHcall.zip ; CGHbase.zip

Version 2.17.4 Bugs from 2.17.2 and 2.17.3 repaired.
These versions are re-submitted to BioC
Linux, Unix, etc [non-tested]: CGHcall.tar.gz
Windows: CGHcall.zip



Use help(package=CGHcall) for help file. Use help(package=CGHcall) for help file. An example script for using the package, versions higher than 2.17.0.
An example script for using the package, versions 2.9.1.to 2.9.3


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)