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

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, benilton 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 > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Successful people ask better questions, and as a result, they get better answers. (Tony Robbins)