snapCGH and CGH method evaluation
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João Fadista ▴ 500
@joao-fadista-1942
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@sean-davis-490
Last seen 3 months ago
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Jo?o 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. > > The "standard" way of doing this is a "frequency plot". Simply sum across samples all the probes that are greater (less) than a certain threshold and plot them along the chromosome. I don't personally like them very much, but it is easy to produce. Also, you might look at the package cghMCR and also at the java executable called STAC. > 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? > This is a very challenging problem. You, as the researcher, will probably need to decide what you think is important (short segments, long segments, high-copy number gains, homozygous deletions, copy number polymorphisms, etc.) and design your own methods for pulling these out. A simple statistical test does not do the trick, in my experience, for pulling out all the relevant information. If you really want something that gives statistical significance, you might want to look at an article by Lipson et al., in RECOMB 2005 (don't have the exact reference at hand). Sean
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Ramon Diaz ★ 1.1k
@ramon-diaz-159
Last seen 10.2 years ago
On Monday 04 December 2006 13:01, Jo?o 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. Best, R. P.S. A new version of the package with a vignette should be available soon (about 10 days?) > > > Best regards > > Jo?o Fadista > Ph.d. student > > > > > Danish Institute of Agricultural Sciences > Research Centre Foulum > Dept. of Genetics and Biotechnology > Blichers All? 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=""/> > > ________________________________ > > News and news media <http: www.agrsci.org="" navigation="" nyheder_og_presse=""> . > > This email may contain information that is confidential. Any use or > publication of this email without written permission from DIAS is not > allowed. If you are not the intended recipient, please notify DIAS > immediately and delete this email. > > > > [[alternative HTML version deleted]] -- Ram?n D?az-Uriarte Bioinformatics Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en s...{{dropped}}
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