[BioC] segmentation for Affy SNP arrays

[Ramon Diaz-Uriarte]

Dear Yu,


The packages that you mention (and some others, too) can be used with Affy SNP 
arrays. The paper by Yu et al., 2007, BMC Bioinformatics,8: 145+ 
(http://www.biomedcentral.com/1471-2105/8/145/abstract), for example, 
compares their performance. (Please note that we have some problems with the 
way our RJaCGH package was used and we are working on a reply. I can send 
further details off-list).

Best,

R.


On Tuesday 18 September 2007 22:38, Yu Chuan Tai wrote:
> Thanks! Looks like aroma.affymetrix uses GLAD model for segmentation......
> Is there any other software available?
>
> Yu Chuan
>
> On Tue, 18 Sep 2007, Kasper Daniel Hansen wrote:
> > You can check out aroma.affymetrix from www.braju.com/R
> >
> > Kasper
> >
> > On Sep 18, 2007, at 12:51 PM, Yu Chuan Tai wrote:
> >> Hi List,
> >>
> >> Just want to know if there is any software which does segmentation
> >> on copy number estimates from Affy SNP arrays? It looks like GLAD,
> >> DNAcopy and snapCGH are only for array CGH......
> >>
> >> Thanks!
> >> Yu Chuan
> >>
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-- 
Ramón Díaz-Uriarte
Statistical Computing Team
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

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
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