Entering edit mode
7.5 years ago
aldoc
▴
10
Hi,
I'm trying to read Illumina idats with crlmm in R, and I get this error:
Error in quantile.default(M, c(1, 5)/6, names = FALSE)
I have found multiple posts about this issue, but none of them seems to provide a general answer:
- https://support.bioconductor.org/p/86109/#96072
- https://support.bioconductor.org/p/78775/
- https://www.researchgate.net/post/How_do_you_retrieve_Genotype_Information_from_a_CEL_file_obtained_from_Gene_Expression_Omnibus_in_R
- https://support.bioconductor.org/p/59895/#59963
In a couple of those links, there are answers suggesting that this is due to small sample sizes, but n=100 in one post, and in my case, n=36. This is the complete output I get in R:
thedata <- genotype.Illumina(cdfName="humanomni25quadv1b", call.method='krlmm')
Instantiate CNSet container.
path arg not set. Assuming files are in local directory, or that complete path is provided
Initializing container for genotyping and copy number estimation
Loading required package: humanomni25quadv1bCrlmm
Welcome to humanomni25quadv1bCrlmm version 1.0.2
Processing sample stratum 1 of 1
'path' arg not set. Assuming files are in local directory, or that complete path is provided in 'arrayNames'
Loading chip annotation information.
Loading reference normalization information.
Quantile normalizing 36 arrays, one at a time.
|======================================================================| 100%
Loading snp annotation and mixture model parameters.
Calibrating 36 arrays.
| | 0%Error in quantile.default(M, c(1, 5)/6, names = FALSE) :
missing values and NaN's not allowed if 'na.rm' is FALSE
Any ideas? Thanks a lot,
