[BioC] segmentation for Affy SNP arrays

[Benjamin Otto]

Hi Yu,

You might also have a look at Dchip, CNAG and GEMCA. Theye are no R packages
but should be able to calculate the CNs for you up to the 500k chips.

However I would like to join Yu here in one point: Is there already any
package which can handle the new SNP6.0 chips? As far as I know not yet, or
is there one?

Regards,

Benjamin






-----Ursprüngliche Nachricht-----
Von: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag von Ramon
Diaz-Uriarte
Gesendet: Wednesday, September 19, 2007 11:10 AM
An: bioconductor at stat.math.ethz.ch
Betreff: Re: [BioC] segmentation for Affy SNP arrays

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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