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Question: Seurat to SingleCellExperiment Converting error in MAC
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gravatar for hamza_karakurt
13 days ago by
hamza_karakurt0 wrote:

Hello everyone,

I just started to work with MAC and using my own computer (Windows) as a tester.

I am trying to convert a Seurat object to SingleCellExperiment with Convert function of Seurat package. It works in Windows but does not work in MAC.

Also, is there a way in Scater package to read 10X files?

My codes are: 

rna.data <- Read10X(data.dir = "C:/Users/hamza/Documents/R/New_Plan/Sample_Data_10X/filtered_gene_bc_matrices/hg19")
rna <- CreateSeuratObject(raw.data = rna.data)

sce <- Convert(from = rna , to = "sce")

keep_feature <- rowSums(counts(sce) > 0) > 0
sce <- sce[keep_feature,]

I use the same codes in MAC but in the "keep_feature" step I have an error which says: 'x' must be an array of at least two dimensions

My session info for MAC:

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.2

Matrix products: default

BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib

LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] scater_1.10.0               SingleCellExperiment_1.4.0  SummarizedExperiment_1.12.0 DelayedArray_0.8.0          BiocParallel_1.16.0         matrixStats_0.54.0         
 [7] Biobase_2.42.0              GenomicRanges_1.34.0        GenomeInfoDb_1.18.0         IRanges_2.16.0              S4Vectors_0.20.0            BiocGenerics_0.28.0        
[13] Seurat_2.3.4                Matrix_1.2-15               cowplot_0.9.3               ggplot2_3.1.0              

loaded via a namespace (and not attached):
  [1] ggbeeswarm_0.6.0         Rtsne_0.13               colorspace_1.3-2         class_7.3-14             modeltools_0.2-22        ggridges_0.5.1           mclust_5.4.1            
  [8] htmlTable_1.12           XVector_0.22.0           base64enc_0.1-3          rstudioapi_0.8           proxy_0.4-22             npsurv_0.4-0             flexmix_2.3-14          
 [15] bit64_0.9-7              mvtnorm_1.0-8            codetools_0.2-15         splines_3.5.1            R.methodsS3_1.7.1        lsei_1.2-0               robustbase_0.93-3       
 [22] knitr_1.20               Formula_1.2-3            jsonlite_1.5             ica_1.0-2                cluster_2.0.7-1          kernlab_0.9-27           png_0.1-7               
 [29] R.oo_1.22.0              HDF5Array_1.10.0         compiler_3.5.1           httr_1.3.1               backports_1.1.2          assertthat_0.2.0         lazyeval_0.2.1          
 [36] lars_1.2                 acepack_1.4.1            htmltools_0.3.6          tools_3.5.1              bindrcpp_0.2.2           igraph_1.2.2             GenomeInfoDbData_1.2.0  
 [43] gtable_0.2.0             glue_1.3.0               RANN_2.6                 reshape2_1.4.3           dplyr_0.7.7              Rcpp_1.0.0               trimcluster_0.1-2.1     
 [50] gdata_2.18.0             ape_5.2                  nlme_3.1-137             DelayedMatrixStats_1.4.0 iterators_1.0.10         fpc_2.1-11.1             gbRd_0.4-11             
 [57] lmtest_0.9-36            stringr_1.3.1            irlba_2.3.2              gtools_3.8.1             DEoptimR_1.0-8           zlibbioc_1.28.0          MASS_7.3-51.1           
 [64] zoo_1.8-4                scales_1.0.0             doSNOW_1.0.16            rhdf5_2.26.0             RColorBrewer_1.1-2       yaml_2.2.0               reticulate_1.10         
 [71] pbapply_1.3-4            gridExtra_2.3            rpart_4.1-13             segmented_0.5-3.0        latticeExtra_0.6-28      stringi_1.2.4            foreach_1.4.4           
 [78] checkmate_1.8.5          caTools_1.17.1.1         bibtex_0.4.2             Rdpack_0.10-1            SDMTools_1.1-221         rlang_0.3.0.1            pkgconfig_2.0.2         
 [85] dtw_1.20-1               prabclus_2.2-6           bitops_1.0-6             lattice_0.20-38          Rhdf5lib_1.4.0           ROCR_1.0-7               purrr_0.2.5             
 [92] bindr_0.1.1              htmlwidgets_1.3          bit_1.1-14               tidyselect_0.2.5         plyr_1.8.4               magrittr_1.5             R6_2.3.0                
 [99] snow_0.4-3               gplots_3.0.1             Hmisc_4.1-1              pillar_1.3.0             foreign_0.8-71           withr_2.1.2              fitdistrplus_1.0-11     
[106] mixtools_1.1.0           RCurl_1.95-4.11          survival_2.43-1          nnet_7.3-12              tibble_1.4.2             tsne_0.1-3               crayon_1.3.4            
[113] hdf5r_1.0.1              KernSmooth_2.23-15       viridis_0.5.1            grid_3.5.1               data.table_1.11.8        metap_1.0                digest_0.6.18           
[120] diptest_0.75-7           tidyr_0.8.2              R.utils_2.7.0            munsell_0.5.0            beeswarm_0.2.3           viridisLite_0.3.0        vipor_0.4.5             

Session info for Windows:

R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=Turkish_Turkey.1254  LC_CTYPE=Turkish_Turkey.1254   
[3] LC_MONETARY=Turkish_Turkey.1254 LC_NUMERIC=C                   
[5] LC_TIME=Turkish_Turkey.1254    

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

other attached packages:
 [1] Seurat_2.3.4                Matrix_1.2-14               cowplot_0.9.3              
 [4] scater_1.10.0               ggplot2_3.1.0               SingleCellExperiment_1.4.0 
 [7] SummarizedExperiment_1.12.0 DelayedArray_0.8.0          BiocParallel_1.16.0        
[10] matrixStats_0.54.0          Biobase_2.42.0              GenomicRanges_1.34.0       
[13] GenomeInfoDb_1.18.0         IRanges_2.16.0              S4Vectors_0.20.0           
[16] BiocGenerics_0.28.0        

loaded via a namespace (and not attached):
  [1] snow_0.4-3               backports_1.1.2          Hmisc_4.1-1             
  [4] plyr_1.8.4               igraph_1.2.2             lazyeval_0.2.1          
  [7] splines_3.5.1            digest_0.6.18            foreach_1.4.4           
 [10] htmltools_0.3.6          viridis_0.5.1            lars_1.2                
 [13] gdata_2.18.0             magrittr_1.5             checkmate_1.8.5         
 [16] cluster_2.0.7-1          mixtools_1.1.0           ROCR_1.0-7              
 [19] R.utils_2.7.0            colorspace_1.3-2         dplyr_0.7.7             
 [22] crayon_1.3.4             RCurl_1.95-4.11          jsonlite_1.5            
 [25] bindr_0.1.1              survival_2.43-1          zoo_1.8-4               
 [28] iterators_1.0.10         ape_5.2                  glue_1.3.0              
 [31] gtable_0.2.0             zlibbioc_1.28.0          XVector_0.22.0          
 [34] kernlab_0.9-27           Rhdf5lib_1.4.0           prabclus_2.2-6          
 [37] DEoptimR_1.0-8           HDF5Array_1.10.0         scales_1.0.0            
 [40] mvtnorm_1.0-8            bibtex_0.4.2             Rcpp_0.12.19            
 [43] metap_1.0                dtw_1.20-1               viridisLite_0.3.0       
 [46] htmlTable_1.12           reticulate_1.10          foreign_0.8-71          
 [49] bit_1.1-14               proxy_0.4-22             mclust_5.4.1            
 [52] SDMTools_1.1-221         Formula_1.2-3            tsne_0.1-3              
 [55] htmlwidgets_1.3          httr_1.3.1               gplots_3.0.1            
 [58] RColorBrewer_1.1-2       fpc_2.1-11.1             acepack_1.4.1           
 [61] modeltools_0.2-22        ica_1.0-2                pkgconfig_2.0.2         
 [64] R.methodsS3_1.7.1        flexmix_2.3-14           nnet_7.3-12             
 [67] tidyselect_0.2.5         rlang_0.3.0.1            reshape2_1.4.3          
 [70] munsell_0.5.0            tools_3.5.1              ggridges_0.5.1          
 [73] stringr_1.3.1            yaml_2.2.0               npsurv_0.4-0            
 [76] knitr_1.20               bit64_0.9-7              fitdistrplus_1.0-11     
 [79] robustbase_0.93-3        caTools_1.17.1.1         purrr_0.2.5             
 [82] RANN_2.6                 bindrcpp_0.2.2           pbapply_1.3-4           
 [85] nlme_3.1-137             R.oo_1.22.0              hdf5r_1.0.1             
 [88] compiler_3.5.1           rstudioapi_0.8           beeswarm_0.2.3          
 [91] png_0.1-7                lsei_1.2-0               tibble_1.4.2            
 [94] stringi_1.2.4            lattice_0.20-35          trimcluster_0.1-2.1     
 [97] pillar_1.3.0             Rdpack_0.10-1            lmtest_0.9-36           
[100] data.table_1.11.8        bitops_1.0-6             irlba_2.3.2             
[103] gbRd_0.4-11              R6_2.3.0                 latticeExtra_0.6-28     
[106] KernSmooth_2.23-15       gridExtra_2.3            vipor_0.4.5             
[109] codetools_0.2-15         MASS_7.3-50              gtools_3.8.1            
[112] assertthat_0.2.0         rhdf5_2.26.0             withr_2.1.2             
[115] GenomeInfoDbData_1.2.0   diptest_0.75-7           doSNOW_1.0.16           
[118] grid_3.5.1               rpart_4.1-13             tidyr_0.8.2             
[121] class_7.3-14             DelayedMatrixStats_1.4.0 segmented_0.5-3.0       
[124] Rtsne_0.13               base64enc_0.1-3          ggbeeswarm_0.6.0        

 

 

Thank you.

ADD COMMENTlink modified 12 days ago by Steve Lianoglou12k • written 13 days ago by hamza_karakurt0
3
gravatar for Steve Lianoglou
13 days ago by
Denali
Steve Lianoglou12k wrote:

I'm pretty sure you are getting the "'x' must be an array of at least two dimensions" error in this code block:

keep_feature <- rowSums(counts(sce) > 0) > 0

Because the counts function is returning a sparse matrix, and you are using the base::rowSums function, which doesn't know how to handle it. The Matrix::rowSums function should do the trick, ie.

library(Matrix)
keep_feature <- Matrix::rowSums(counts(sce) > 0) > 0

Also, you will find a read10xCounts function in the DropletUtils package that will load up a 10x dataset into a SingleCellExperiment.

ADD COMMENTlink modified 12 days ago • written 13 days ago by Steve Lianoglou12k

Thank you so much. It worked.

ADD REPLYlink written 12 days ago by hamza_karakurt0
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