monocle: Error in if (cds@expressionFamily@vfamily %in% c("negbinomial", "negbinomial.size"))
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Entering edit mode
@mehmet-ilyas-cosacak-9020
Last seen 3.6 years ago
Germany/Dresden/ CRTD - DZNE

Hi,

I have a problem runing monocle. The error is as below:

> es.mef <- reduceDimension(es.mef,use_irlba = F) # Reduce dimensionality
Error in if (cds@expressionFamily@vfamily %in% c("negbinomial", "negbinomial.size")) { :
  argument is of length zero

Has anyone had a problem like that or know what is the problem??

I have the problem even if  I use the data-set for tutorial of monocle as well. So it is not because of my dataset from scRNA-Seq.

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
 [1] grid      splines   parallel  stats4    stats     graphics  grDevices utils     datasets 
[10] methods   base     

other attached packages:
 [1] monocle_2.6.1              DDRTree_0.1.5              BiocInstaller_1.28.0      
 [4] HSMMSingleCell_0.112.0     plyr_1.8.4                 reshape2_1.4.3            
 [7] fastICA_1.2-1              combinat_0.0-8             igraph_1.1.2              
[10] irlba_2.3.2                Matrix_1.2-12              VGAM_1.0-5                
[13] SingleCellExperiment_1.0.0 SummarizedExperiment_1.8.1 DelayedArray_0.4.1        
[16] GenomicRanges_1.30.0       GenomeInfoDb_1.14.0        ggplot2_2.2.1             
[19] org.Dr.eg.db_3.5.0         AnnotationDbi_1.40.0       IRanges_2.12.0            
[22] S4Vectors_0.16.0           Biobase_2.38.0             BiocGenerics_0.24.0       
[25] Rtsne_0.13                 matrixStats_0.53.0        

loaded via a namespace (and not attached):
 [1] viridis_0.5.0          httr_1.3.1             bit64_0.9-7            viridisLite_0.3.0     
 [5] shiny_1.0.5            assertthat_0.2.0       blob_1.1.0             GenomeInfoDbData_1.0.0
 [9] ggrepel_0.7.0          slam_0.1-42            progress_1.1.2         pillar_1.1.0          
[13] RSQLite_2.0            lattice_0.20-35        limma_3.34.8           glue_1.2.0            
[17] densityClust_0.3       digest_0.6.15          RColorBrewer_1.1-2     XVector_0.18.0        
[21] colorspace_1.3-2       htmltools_0.3.6        httpuv_1.3.5           XML_3.98-1.9          
[25] pkgconfig_2.0.1        pheatmap_1.0.8         qlcMatrix_0.9.5        biomaRt_2.34.2        
[29] zlibbioc_1.24.0        xtable_1.8-2           scales_0.5.0           RANN_2.5.1            
[33] tibble_1.4.2           lazyeval_0.2.1         magrittr_1.5           mime_0.5              
[37] memoise_1.1.0          FNN_1.1                shinydashboard_0.6.1   tools_3.4.3           
[41] data.table_1.10.4-3    prettyunits_1.0.2      stringr_1.2.0          munsell_0.4.3         
[45] cluster_2.0.6          bindrcpp_0.2           compiler_3.4.3         rlang_0.1.6           
[49] RCurl_1.95-4.10        labeling_0.3           bitops_1.0-6           gtable_0.2.0          
[53] DBI_0.7                R6_2.2.2               gridExtra_2.3          dplyr_0.7.4           
[57] bit_1.1-12             bindr_0.1              stringi_1.1.6          Rcpp_0.12.15  
monocle • 625 views
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Entering edit mode
@mehmet-ilyas-cosacak-9020
Last seen 3.6 years ago
Germany/Dresden/ CRTD - DZNE

The problem is: there are several changes in the functions of monocle. For instance;

es.mef <- new("CellDataSet",as.matrix(expression.data), phenoData = pd,featureData = fd, expressionFamily = negbinomial())

es.mef <- newCellDataSet(as.matrix(expression.data), phenoData = pd,featureData = fd, expressionFamily = negbinomial())

this effects down stream analysis.

fyi.

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