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!