[BioC] Illumina CytoSNP-12 CDF file for crlmm

Benilton Carvalho beniltoncarvalho at gmail.com
Wed Aug 17 19:07:34 CEST 2011

Hi Stephen,

CDF files are exclusive for Affymetrix arrays. So, your question is
how could you create an annotation package that would allow crlmm to
handle properly your Illumina chips.

Currently. this is not a simple task: you would need access to HapMap
data on this particular array. With the HapMap data available, we
would need to train the algorithm (we have code for this, but requires
some manual intervention) and, only then, create the annotation
package you need.

If you're able to get HapMap data for this chip, please contact me
off-list and I may be able to help you out,


On 16 August 2011 14:09, Stephen Rudd <stephen at neuramatix.com> wrote:
> Dear Bioconductor users
> I have the results from a large study based on the Illumina CytoSNP-12 chip that I would like to process in Bioconductor using the crlmm package.
> I can load the results into an NChannelSet object using the crlmm package; the next challenge is the genotyping. There does not appear to be an existing CDF file for this array platform. I have tried the related humanomniexpress12v1b CDF but it is not appropriate having twice the number of features and dies with
> Error in chol.default(crossprod(sweep(matS, 1, z[, 1], FUN = "*"), matS)) :
>  the leading minor of order 3 is not positive definite
> I would welcome some insight or recommendations as to how I might build my own CDF file for this array platform.
> Thanks
> Stephen
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