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