Hi,
  Did u try the CNVtools package?
Thanks
Samarjeet

On Wed, Oct 19, 2011 at 4:12 PM, cstrato <cstrato@aon.at> wrote:

> Dear Jim,
>
> Thank you for mentioning xps, however xps does only work for expression
> arrays and not for mapping arrays such as SNP6.
>
> Best regards
> Christian
>
>
>
> On 10/19/11 10:51 PM, James W. MacDonald wrote:
>
>> Hi John,
>>
>> On 10/19/2011 2:27 PM, John linux-user wrote:
>>
>>> Hello,
>>>
>>> Can you please suggest R packages for analyzing affy SNP 6 and 250K as
>>> well as copy number variations for sequencing data? Thanks.
>>>
>>
>> The oligo package will do this (although I don't know if it can do the
>> CNV part). You might also look at xps.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>>> John
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