Error running CellMix SampleAnalysis vignette
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@gaborhalasz-12176
Last seen 4.8 years ago

Dear all,

I'm getting the following error when running the SampleAnalysis vignette of the CellMix package:

library(CellMix)
biocLite("GEOquery")
acr <- ExpressionMix("GSE20300", verbose = 2)
res <- gedBlood(acr, verbose = 2);
###...skipping most of the output...
###Normalizing signatures and target together (method: quantiles) ... OK
Error in (function (od, vd)  : 
            object and replacement value dimnames differ

biocVersion() is 3.4, and my sessionInfo() is:

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.5 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] stats4    compiler  parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GEOquery_2.40.0      hgu133b.db_3.2.3     hgu133a.db_3.2.3     org.Hs.eg.db_3.4.0  
 [5] CellMix_1.6.2        GSEABase_1.36.0      graph_1.52.0         annotate_1.52.1     
 [9] XML_3.98-1.5         AnnotationDbi_1.36.1 IRanges_2.8.1        S4Vectors_0.12.1    
[13] stringr_1.1.0        csSAM_1.2.4          NMF_0.20.6           Biobase_2.34.0      
[17] BiocGenerics_0.20.0  cluster_2.0.4        rngtools_1.2.4       pkgmaker_0.22       
[21] registry_0.3         BiocInstaller_1.24.0

loaded via a namespace (and not attached):
 [1] genefilter_1.56.0     gtools_3.5.0          beeswarm_0.2.3        lpSolve_5.6.13       
 [5] reshape2_1.4.2        splines_3.3.1         lattice_0.20-33       limSolve_1.5.5.1     
 [9] colorspace_1.3-2      survival_2.40-1       DBI_0.5-1             RColorBrewer_1.1-2   
[13] matrixStats_0.51.0    foreach_1.4.3         plyr_1.8.4            munsell_0.4.3        
[17] gtable_0.2.0          codetools_0.2-15      memoise_1.0.0         doParallel_1.0.10    
[21] preprocessCore_1.36.0 Rcpp_0.12.9           xtable_1.8-2          corpcor_1.6.8        
[25] scales_0.4.1          ggplot2_2.2.1         digest_0.6.11         stringi_1.1.2        
[29] grid_3.3.1            bibtex_0.4.0          quadprog_1.5-5        tools_3.3.1          
[33] bitops_1.0-6          magrittr_1.5          lazyeval_0.2.0        RCurl_1.95-4.8       
[37] tibble_1.2            RSQLite_1.1-2         MASS_7.3-45           Matrix_1.2-6         
[41] gridBase_0.4-7        httr_1.2.1            assertthat_0.1        iterators_1.0.8      
[45] R6_2.2.0   

Any help would be greatly appreciated.  Thanks,

Gabor

 

software error cellmix vignette expressionset • 1.3k views
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Note, the function does work if you explicitly pass it the expression matrix directly rather than the acr ExpressionMix class object:

res <- gedBlood(acr@assayData$exprs, verbose = TRUE)
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Thank you so much!!  Passing in the expression matrix directly works for me as well.  (And otherwise yes, that is the line that breaks, and it may work with previous Biobase versions).  

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I've found exactly the same thing.

The error seems to be coming from a validation check in the Biobase package: https://github.com/Bioconductor-mirror/Biobase/blob/master/R/methods-eSet.R#L461

I ran debug on gedBlood() and then gedProportions() and found that it happens on this line of code: https://github.com/rforge/cellmix/blob/master/pkg/CellMix/R/ged.R#L769 . It seems a strange error as the previous line tries to set the dimnames equal to each other.

Perhaps a compatibility issue with a new version of Biobase? The vignette says it uses Biobase 2.20.0. I haven't been able to confirm this by installing that old version of Biobase - anyone know an easy way to do that?

I have emailed the package maintainer last week but haven't heard back yet.

Graeme

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