[BioC] Illumina CytoSNP-12 CDF file for crlmm

Stephen Rudd stephen at neuramatix.com
Tue Aug 16 15:09:39 CEST 2011

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.



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