[BioC] CRLMM Annotation file

[James W. MacDonald]

Hi Venu,

My bad! Looks like crlmm works for the Illumina platform as well. I 
guess that shows how long it's been since I did any SNP work...

Best,

Jim


On 2/26/2014 12:53 PM, Venu Pullabhatla wrote:
> Hi Jim
>
> Many thanks for your prompt response. I am surprised to know about 
> crlmm specificity to Affymetrix because the vignette claims to be 
> applicable for Illumina platforms also. I am referring to the 
> following vignette.
>
> http://www.bioconductor.org/packages/release/bioc/vignettes/crlmm/inst/doc/IlluminaPreprocessCN.pdf 
>
>
> I have come across beadArraySNP package, but if I am correct, this 
> package needs text files imported from Genome Studio software. Can you 
> please suggest any other package(s) that could read raw IDAT files 
> perform CNV and LOH analysis. Many thanks.
>
> Best wishes
>
> Venu
>
> On 26/02/14 17:42, James W. MacDonald wrote:
>> Hi Venu,
>>
>> The crlmm package is intended for Affymetrix arrays, not Illumina. I 
>> believe you want the beadArraySNP package.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>> On Wednesday, February 26, 2014 12:37:06 PM, Venu Pullabhatla wrote:
>>> Hi All
>>>
>>> I am working on Illumina HumanOmni5MExome-4v1-1_A SNP array to
>>> identify CNV's and LOH's from this data. I have come across "crlmm"
>>> package that can do this and started following the "Preprocessing and
>>> Genotyping Illumina Arrays for Copy Number Analysis" vignette. I
>>> realized that the crlmm package does not include CDF annotation for
>>> this Illumina array. I tried to find this on the Bioconductor site and
>>> did not succeed. Can anyone please help me where I can find this
>>> annotation file or a way I can prepare one myself. Any help is very
>>> much appreciated. Many thanks.
>>>
>>> Venu
>>>
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>>
>> -- 
>> James W. MacDonald, M.S.
>> Biostatistician
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099