crlmm crossprod error, and missing files in annotation
2
0
Entering edit mode
@andrewjskelton73-7074
Last seen 23 months ago
United Kingdom

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.

crlmm • 863 views
1
Entering edit mode
Matthew Ritchie ▴ 1000
@matthew-ritchie-650
Last seen 5 months ago
Australia

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.

0
Entering edit mode

Hi Matt, no these are in fact OmniExpress12v1b (according to the sample sheet) - There's 24 IDAT files per barcode, so divide that by 2 for the red and green channels = 12. - I received 2 projects, one on the OmniExpress12v1b, and another on the OmniExpress24v1b

0
Entering edit mode
Matthew Ritchie ▴ 1000
@matthew-ritchie-650
Last seen 5 months ago
Australia

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

0
Entering edit mode

I'd really appreciate that! If you drop me an email at andrew.skelton[at]ncl.ac.uk I'll arrange them to be sent over