CellMix - Custom matrix with Abbas signature
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carleshf ▴ 10
Last seen 6.6 years ago

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)
[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                
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  
deconvolution cellmix • 1.6k views

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