[BioC] CRLMM Annotation file

[Venu Pullabhatla]

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


-- 
Venu Pullabhatla, Ph.D.
Senior Bioinformatician
NIHR GSTFT/KCL Comprehensive Biomedical Research Centre
Guy's & St. Thomas' NHS Foundation Trust
Guy's Hospital, Tower Wing, 16th Floor
Great Maze Pond, London SE1 9RT
Phone: 0044(0)2071887188 (x53378)