[BioC] segmentation for Affy SNP arrays

[Yu Chuan Tai]

Hi Ramon,

Thanks for your info. I will look at the paper you mentioned below and get 
back to you if I need more details about your package.

Best,
Yu Chuan

On Wed, 19 Sep 2007, Ramon Diaz-Uriarte wrote:

> 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)
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>
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>
>
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