I am trying to call genotypes with crlmm package version 1.28.2. My SNP array data was obtained using the following Illumina platforms:
- HumanCytoSNP-12 V2.1 (Annotation package: humancytosnp12v2p1h)
- HumanOmni2.5-8 V1-1 (Annotationpackage: humanomni258v1p1b)
What I am doing is:
samplesheet <- read.csv(paste(path, sheet, sep = "/"), header=TRUE, stringsAsFactors=FALSE)
idats <- readIdatFiles(sampleSheet=samplesheet, path=paste(prefix, path, sep="/")) crlmmOut <- crlmmIllumina(RG=idats, cdfName=cdf)
cdf is the name of the corresponding annotation package.
I have 2 different problems for each annotation package mentioned.
Human CytoSNP-12 V2.1
The genotyping is carried out without errors but with a warning issued:
In crlmmGT(A = res[["A"]], B = res[["B"]], SNR = res[["SNR"]], mixtureParams = res[["mixtureParams"]], : Recalibration not possible. Possible cause: small sample size.
The called genotypes however (when accessed through
calls()) are absurd: all of them are some random integers in the 1000s range, instead of expected class labels. Here just the first six entries of
> head(calls) H005-K6J1-T1-D1 H005-CSGD-T1-D1 H005-WHY2-T1-D1 H005-0QYL-T1-D1 H005-4M10-T1-D1 rs10059646 1688 10790 11933 12221 12016 rs10084637 10352 9991 9976 10359 10400 rs10111087 918 889 1047 17698 10882 rs10166589 1206 1349 1164 1186 1297 rs10166677 1038 876 1010 901 4000 rs10200219 7257 1185 6788 7370 7354
Human Omni2.5-8 V1-1
Here I actually get an error message:
Error in solve.default(SS) : Lapack routine dgesv: system is exactly singular: U[3,3] = 0 Calls: genotypeArrayData -> crlmmIllumina -> crlmmGT -> solve -> solve.default Execution halted
I printed the
SS matrices from
crlmmGT function and all the entries were
There is a suspicious line (136 in crlmm-functions.R):
newparams[["centers"]][newparams[["N"]] < minN] <- NA
Perhaps all entries in
newparams become set to
NA? Sorry, I haven't looked too deep into the code. I was just wondering, if I am missing something very simple, which leads to these problems.
Thank you! --- Vlad
> sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.5 (Final) locale:  LC_CTYPE=C 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:  ff_2.2-13 bit_1.1-12 crlmm_1.28.2  preprocessCore_1.32.0 oligoClasses_1.32.0 loaded via a namespace (and not attached):  Rcpp_0.12.3 XVector_0.10.0  splines_3.2.3 GenomicRanges_1.22.3  BiocGenerics_0.16.1 zlibbioc_1.16.0  IRanges_2.4.6 ellipse_0.3-8  lattice_0.20-33 foreach_1.4.3  GenomeInfoDb_1.6.2 base64_1.1  grid_3.2.3 SummarizedExperiment_1.0.2  parallel_3.2.3 Biobase_2.30.0  DBI_0.3.1 matrixStats_0.50.1  iterators_1.0.8 RcppEigen_0.3.2.7.0  affyio_1.40.0 Matrix_1.2-3  S4Vectors_0.8.7 codetools_0.2-14  VGAM_1.0-0 RSQLite_1.0.0  BiocInstaller_1.20.1 Biostrings_2.38.3  stats4_3.2.3 mvtnorm_1.0-4  illuminaio_0.12.0