I am trying to analyze some Illumina beadarray SNP data (human1mv1c) using crlmm and I keep running into the error shown below. Since my previous attempts on a second, independent cohort (using the human1mduov3b chip) succeeded, my guess is that the problem resides somewhere in the analysis setup and not the function itself. Furthermore, I saw an earlier post with the same issue and error, which was due to the fact that unsupported Illumina GoldenGate chips were used:
Another post with a similar error was non-conclusive:
Thank you in advance, any help is greatly appreciated.
library(crlmm) library(ff) sampleSXS = read.csv("SXS_sample_map.csv",header=TRUE, as.is=TRUE) sampleSXS[1:5,] Sample_ID SentrixBarcode SentrixPosition Gender E320-45N 4040350100 A M E320-45T 4040350189 A M E321-39N 4040350200 A M E321-39T 4040350169 A M E323-08N 4040350176 A M arrayInfo = list(barcode=NULL, position="SentrixPosition") cdfName = "human1mv1c" batch = rep("1", nrow(sampleSXS)) arrayNames = paste(sampleSXS[,2],sampleSXS[,3],sep="_") cnSetSXS = genotype.Illumina(sampleSheet=sampleSXS, arrayNames=arrayNames, arrayInfoColNames=arrayInfo,cdfName=cdfName,batch=batch) 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 Processing sample stratum 1 of 1 path arg not set. Assuming files are in local directory, or that complete path is provided Quantile normalizing 24 arrays by 20 strips. |======================================================================| 100% Calibrating 24 arrays. | | 0%Error in chol.default(crossprod(sweep(matS, 1, z[, 1], FUN = "*"), matS)) : the leading minor of order 1 is not positive definite sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-pc-linux-gnu (64-bit) locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  human1mv1cCrlmm_1.0.3 human1mduov3bCrlmm_1.0.4 ff_2.2-13  bit_1.1-12 crlmm_1.24.0 preprocessCore_1.28.0  oligoClasses_1.28.0 loaded via a namespace (and not attached):  affyio_1.34.0 base64_1.2 Biobase_2.26.0  BiocGenerics_0.12.1 BiocInstaller_1.16.1 Biostrings_2.34.1  codetools_0.2-10 ellipse_0.3-8 foreach_1.4.2  GenomeInfoDb_1.2.4 GenomicRanges_1.18.4 grid_3.1.2  illuminaio_0.8.0 IRanges_2.0.1 iterators_1.0.7  lattice_0.20-30 Matrix_1.1-5 matrixStats_0.14.0  mvtnorm_1.0-2 parallel_3.1.2 Rcpp_0.11.4  RcppEigen_0.3.2.3.0 S4Vectors_0.4.0 splines_3.1.2  stats4_3.1.2 tools_3.1.2 VGAM_0.9-6  XVector_0.6.0 zlibbioc_1.12.0