[BioC] snapCGH and CGH method evaluation

Ramon Diaz-Uriarte rdiaz at cnio.es
Mon Dec 4 14:28:07 CET 2006

On Monday 04 December 2006 13:01, João Fadista wrote:
> Dear all,
> snapCGH -> Does anyone know how to display regions of gain or loss across
> multiple samples in the same plot? I am asking this with the purpose of
> finding common breakpoints and regions of common gain or loss between
> samples.
> CGH method evaluation -> Does anyone knows if there is any CGH package that
> estimate the statistical significance of the detected copy number changes
> and then rank them accordingly?

Dear Joao,

My answers do not refer to snapCGH, but to our package RJaCGH 
(http://cran.r-project.org/src/contrib/Descriptions/RJaCGH.html) which might 
provide some of what you want.

For the first, if you use an "array" object, the default plot shows the 
frequency with which each alteration is present over the set of samples. 

For the second, we use a Bayesian approach via MCMC, so we return the 
posterior probabilities of alteration for every gene. You can then rank them, 
or select those above a certain threshold, etc, however you want.



P.S. A new version of the package with a vignette should be available soon 
(about 10 days?)

> Best regards
> João Fadista
> Ph.d. student
>  	 Danish Institute of Agricultural Sciences
> Research Centre Foulum
> Dept. of Genetics and Biotechnology
> Blichers Allé 20, P.O. BOX 50
> DK-8830 Tjele
> Phone:	 +45 8999 1900
> Direct:	 +45 8999 8999
> E-mail:	 Joao.Fadista at agrsci.dk <mailto:Joao.Fadista at agrsci.dk>
> Web:	 www.agrsci.org <http://www.agrsci.org/>
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Ramón Díaz-Uriarte
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

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