Question: Illumina CanineHD CNV & crlmm?
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gravatar for Matthew Ritchie
9.0 years ago by
Australia
Matthew Ritchie800 wrote:
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, Matt > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
go hapmap cdf affy crlmm • 695 views
ADD COMMENTlink written 9.0 years ago by Matthew Ritchie800
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