Hi, 

I'm working with some humanomniexpress12v1b chips, and I've run the following basic command:

cnSet <- genotype.Illumina(sampleSheet       = sample_sheet,
                           path              = "tmp/IDAT/subset/",
                           cdfName           = 'humanomniexpress12v1b',
                           call.method       = "crlmm",
                           copynumber        = T,
                           quantile.method   = "between")

Which yields the error:

Error in chol.default(crossprod(sweep(matS, 1, z[, 1], FUN = "*"), matS)) : 
  the leading minor of order 1 is not positive definite

I've tried subsetting, and just reading in one barcode, then another, but I still get the same error each time. I tried an alternative normalisation (within), which produces the following error:

Loading reference normalization information.
Error in loader("targetXY.rda", .crlmmPkgEnv, pkgname) : 
  File /home/andrew/R/x86_64-pc-linux-gnu-library/3.2/humanomniexpress12v1bCrlmm/extdata/targetXY.rda does not exist in humanomniexpress12v1bCrlmm

I've checked, and the file isn't there. I'm stumped, and with no alternatives to reading IDAT files for genotype chips, I guess I'll be forced to utilise genome studio. 

Any advice is welcome! 

Are these OmniExpress24v1 chips referred to in your previous post? The OmniExpress12v1b package you're using above probably won't work for this platform as the probe IDs are likely to be different. We need to add a more informative error message here, but it generally arises when a chip type mismatch has occurred.

Hmm - not sure then. If you can provide a few examples IDAT files offline, I will take a closer look.