CellMix - Custom matrix with Abbas signature
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carleshf ▴ 10
@carleshf-7416
Last seen 4.2 years ago
Spain/Barcelona/ISGlobal

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  
deconvolution cellmix • 1.2k views
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