[BioC] Illumina CanineHD CNV & crlmm?

Matthew Ritchie mritchie at wehi.EDU.AU
Sat Dec 4 15:44:13 CET 2010

Hi Karl,

Thanks for your query and apologies for the delay in replying.

A current limitation with crlmm is that training data is required.  For
humans, HapMap data can be used as Illumina generally run all or some of
these samples on each chip type and the 'true' calls can be downloaded
separately.  For other species, there isn't such a resource available
(DogMap/CowMap?) so we can't easily generate a region package for these
arrays.  So unfortunately you aren't able to use crlmm to analyze your
canine data at this time.

Best wishes,


> Dear Dr. Ritchie and Bioconductor users,
> Has anyone succeeded in loading data from the Illumina CanineHD CNV bead
> array into Bioconductor? I think the crlmm package is what I should use
> but there is no existing CDF for this array. I downloaded the annotations
> from the Illumina FTP site but I'm not exactly sure how to go about
> creating a CDF from those files as all of the CDF creation packages refer
> to the Affy platform. Any suggestions or comments would be greatly
> appreciated. Thanks in advance!
> http://www.illumina.com/products/caninehd_whole_genome_genotyping.ilmn
> -------------------------------------------
> Karl Dykema
> Computational Biologist
> Van Andel Research Institute
> 333 Bostwick Ave NE
> Grand Rapids, MI 49503

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