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


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



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
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
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