Question: Error genotyping with CRLMM
0
gravatar for stuti.agrawal
3.6 years ago by
United States
stuti.agrawal0 wrote:

Hi,

I am trying to perform copy number analysis on some methylation data (idat format) from TCGA. These are on a Illumina HumanMethylation27k chip. I am facing the following errors using CRLMM. Could you please guide me on how to go about using CRLMM for this data?

> t <- genotype.Illumina(path="/Users/stuti/test_idat/DNA_Methylation/JHU_USC__HumanMethylation27/Level_1/", cdfName = "human370v1c")
Instantiate CNSet container.
Initializing container for genotyping and copy number estimation
Loading required package: human370v1cCrlmm
Welcome to human370v1cCrlmm version 1.0.2
Processing sample stratum 1 of 1
Loading chip annotation information.
Quantile normalizing 1 arrays by 12 strips.
  |================================================================================================================| 100%
Loading snp annotation and mixture model parameters.
Calibrating 1 arrays.
  |                                                                                                                |   0%
Error in chol.default(crossprod(sweep(matS, 1, z[, 1], FUN = "*"), matS)) : 
  the leading minor of order 1 is not positive definite

Thanks,

Stuti

crlmm copynumber illumina • 543 views
ADD COMMENTlink modified 3.6 years ago by andrew.j.skelton73310 • written 3.6 years ago by stuti.agrawal0
Answer: Error genotyping with CRLMM
1
gravatar for andrew.j.skelton73
3.6 years ago by
United Kingdom
andrew.j.skelton73310 wrote:

The chip manifest you added in as a parameter (human370v1c), doesn't match the data you have (humanMethylation27K)

ADD COMMENTlink written 3.6 years ago by andrew.j.skelton73310
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 358 users visited in the last hour