Entering edit mode
Dear all,
I'm using the package CellMix to deconvolute an expression matrix. What I'm doing is call directly the function gedBlood
with my expression matrix, like this:
res <- gedBlood(e, verbose=TRUE)
But I get this error:
Loading basis signature from Abbas et al. (2009) ... OK [359 features x 17 cell types] Estimating proportions for blood cell subset(s): WB Mapping signature ids onto target ids (method: auto) ... Error in if (checkCode == 63) { : missing value where TRUE/FALSE needed
I run a couple of times CellMix
before, with other arrays and I never got this error. Some ideas hot to solve this?
My sessionInfo:
R version 3.2.0 (2015-04-16) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: CentOS release 6.6 (Final) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=es_ES.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=es_ES.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 compiler parallel stats graphics grDevices utils datasets methods base other attached packages: [1] CellMix_1.6.2 GSEABase_1.30.2 graph_1.46.0 annotate_1.46.0 XML_3.98-1.2 AnnotationDbi_1.30.1 [7] GenomeInfoDb_1.4.0 IRanges_2.2.3 S4Vectors_0.6.0 stringr_1.0.0 csSAM_1.2.4 NMF_0.20.6 [13] cluster_2.0.1 rngtools_1.2.4 pkgmaker_0.22 registry_0.2 biomaRt_2.24.0 Biobase_2.28.0 [19] BiocGenerics_0.14.0 loaded via a namespace (and not attached): [1] Rcpp_0.11.6 BiocInstaller_1.18.3 RColorBrewer_1.1-2 plyr_1.8.2 bitops_1.0-6 [6] iterators_1.0.7 tools_3.2.0 digest_0.6.8 preprocessCore_1.30.0 RSQLite_1.0.0 [11] gtable_0.1.2 gridBase_0.4-7 bibtex_0.4.0 foreach_1.4.2 DBI_0.3.1 [16] beeswarm_0.2.0 proto_0.3-10 genefilter_1.50.0 gtools_3.5.0 grid_3.2.0 [21] limSolve_1.5.5.1 survival_2.38-1 corpcor_1.6.7 ggplot2_1.0.1 reshape2_1.4.1 [26] magrittr_1.5 matrixStats_0.14.0 splines_3.2.0 scales_0.2.4 codetools_0.2-11 [31] MASS_7.3-40 lpSolve_5.6.11 xtable_1.7-4 colorspace_1.2-6 quadprog_1.5-5 [36] stringi_0.4-1 RCurl_1.95-4.6 doParallel_1.0.8 munsell_0.4.2