[BioC] SNP 6 chip

[Benilton Carvalho]

for 250K, you can genotype with the CRLMM algorithm in oligo.

for SNP 6.0, use the crlmm package instead... the implementation
currently available there is an upgrade of the one in oligo, using
features exclusive for SNP 6.0... the crlmm package also offers a CN
tool (details on the vignette).

b

On 19 October 2011 22:12, cstrato <cstrato at 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
>>> [[alternative HTML version deleted]]
>>>
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>
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