cnSet <- genotype.Illumina(sampleSheet=samplesheet[418:425,],arrayNames=arrayNames[418:425],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: humanomni5quadv1bCrlmm Welcome to humanomni5quadv1bCrlmm version 1.0.0 Processing sample stratum 1 of 1 'path' arg not set. Assuming files are in local directory, or that complete path is provide Loading chip annotation information. Loading reference normalization information. Quantile normalizing 8 arrays, one at a time. |======================================================================| 100% Loading snp annotation and mixture model parameters. Calibrating 8 arrays. |======================================================================| 100% Finished preprocessing. Begin genotyping... Start computing log-ratios -- Processing segment 1 out of 9 -- Processing segment 2 out of 9 -- Processing segment 3 out of 9 -- Processing segment 4 out of 9 -- Processing segment 5 out of 9 -- Processing segment 6 out of 9 -- Processing segment 7 out of 9 -- Processing segment 8 out of 9 -- Processing segment 9 out of 9 Done computing log-ratios Leaving out non-variant SNPs Start calculating prior means Done calculating prior means Retrieving defined platform-specific coefficients to predict number of clusters Start predicting number of clusters Error in predictKwithVGLM(VGLMparameters, krlmmCoefficients, verbose) : can't find 'VGLMparameters'