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Problem with Data - Can you please put a simple dataset? #87

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neuhausi opened this issue May 2, 2024 · 0 comments
Open

Problem with Data - Can you please put a simple dataset? #87

neuhausi opened this issue May 2, 2024 · 0 comments

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@neuhausi
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neuhausi commented May 2, 2024

library(Seurat)
library(ggplot2)
library(sctransform)
library(SeuratData)
...

InstallData("pbmc3k")
...

data("pbmc3k")
pbmc3k
Error: Please run UpdateSeuratObject on your object
Error during wrapup: no slot of name "images" for this object of class "Seurat"
Error: no more error handlers available (recursive errors?); invoking 'abort' restart

....

pbmc3k = UpdateSeuratObject(pbmc3k)

...

pbmc3k
An object of class Seurat 
13714 features across 2700 samples within 1 assay 
Active assay: RNA (13714 features, 0 variable features)
 2 layers present: counts, data


pbmc <- CreateSeuratObject(counts = pbmc3k)
Warning: Data is of class Seurat. Coercing to dgCMatrix.
Error in UseMethod(generic = "as.sparse", object = x) : 
  no applicable method for 'as.sparse' applied to an object of class "Seurat"

....

sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.4.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

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

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] cbmc.SeuratData_3.1.4   pbmc3k.SeuratData_3.1.4 SeuratData_0.2.2.9001   sctransform_0.4.1       ggplot2_3.5.1          
[6] Seurat_5.0.3            SeuratObject_5.0.1      sp_2.1-4               

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3     rstudioapi_0.16.0      jsonlite_1.8.8         magrittr_2.0.3         spatstat.utils_3.0-4   rmarkdown_2.26        
  [7] fs_1.6.4               vctrs_0.6.5            ROCR_1.0-11            memoise_2.0.1          spatstat.explore_3.2-7 usethis_2.2.3         
 [13] htmltools_0.5.8.1      curl_5.2.1             parallelly_1.37.1      KernSmooth_2.23-22     desc_1.4.3             htmlwidgets_1.6.4     
 [19] ica_1.0-3              plyr_1.8.9             plotly_4.10.4          zoo_1.8-12             cachem_1.0.8           igraph_2.0.3          
 [25] mime_0.12              lifecycle_1.0.4        pkgconfig_2.0.3        Matrix_1.7-0           R6_2.5.1               fastmap_1.1.1         
 [31] fitdistrplus_1.1-11    future_1.33.2          shiny_1.8.1.1          digest_0.6.35          colorspace_2.1-0       ps_1.7.6              
 [37] patchwork_1.2.0        tensor_1.5             RSpectra_0.16-1        irlba_2.3.5.1          pkgload_1.3.4          progressr_0.14.0      
 [43] fansi_1.0.6            spatstat.sparse_3.0-3  httr_1.4.7             polyclip_1.10-6        abind_1.4-5            compiler_4.4.0        
 [49] remotes_2.5.0          withr_3.0.0            fastDummies_1.7.3      pkgbuild_1.4.4         MASS_7.3-60.2          canvasXpress_1.43.7   
 [55] rappdirs_0.3.3         sessioninfo_1.2.2      tools_4.4.0            lmtest_0.9-40          httpuv_1.6.15          future.apply_1.11.2   
 [61] goftest_1.2-3          glue_1.7.0             callr_3.7.6            nlme_3.1-164           promises_1.3.0         grid_4.4.0            
 [67] Rtsne_0.17             cluster_2.1.6          reshape2_1.4.4         generics_0.1.3         gtable_0.3.5           spatstat.data_3.0-4   
 [73] tidyr_1.3.1            data.table_1.15.4      utf8_1.2.4             spatstat.geom_3.2-9    RcppAnnoy_0.0.22       ggrepel_0.9.5         
 [79] RANN_2.6.1             pillar_1.9.0           stringr_1.5.1          spam_2.10-0            RcppHNSW_0.6.0         later_1.3.2           
 [85] splines_4.4.0          dplyr_1.1.4            lattice_0.22-6         survival_3.5-8         deldir_2.0-4           tidyselect_1.2.1      
 [91] miniUI_0.1.1.1         pbapply_1.7-2          knitr_1.46             gridExtra_2.3          scattermore_1.2        xfun_0.43             
 [97] devtools_2.4.5         matrixStats_1.3.0      stringi_1.8.3          lazyeval_0.2.2         yaml_2.3.8             evaluate_0.23         
[103] codetools_0.2-20       tibble_3.2.1           cli_3.6.2              uwot_0.2.2             xtable_1.8-4           reticulate_1.36.1     
[109] processx_3.8.4         munsell_0.5.1          Rcpp_1.0.12            globals_0.16.3         spatstat.random_3.2-3  png_0.1-8             
[115] parallel_4.4.0         ellipsis_0.3.2         dotCall64_1.1-1        profvis_0.3.8          urlchecker_1.0.1       listenv_0.9.1         
[121] viridisLite_0.4.2      scales_1.3.0           ggridges_0.5.6         crayon_1.5.2           leiden_0.4.3.1         purrr_1.0.2           
[127] rlang_1.1.3            cowplot_1.1.3         

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