Error in is.factor: no slot of name "data" for this object of class "Assay5"

[nick-youngblut]

I'm trying to load the pbmc_1K_singleCellRNA.h5 dataset. I'm simply selecting the h5 file in the Please select a file (H5 / plaint text / RDS) and click on 'Load dataset': loader, and then clicking the Load dataset button. The error:

Warning: Error in is.factor: no slot of name "data" for this object of class "Assay5"
  1: runApp
Warning: Error in if: argument is of length zero
  1: runApp

sessionInfo

R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
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/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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/Los_Angeles
tzcode source: internal

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

other attached packages:
 [1] scCATCH_3.2.2        glmGamPoi_1.14.3     sctransform_0.4.1    BiocParallel_1.36.0 
 [5] stringr_1.5.1        HH_3.1-52            multcomp_1.4-26      TH.data_1.1-2       
 [9] MASS_7.3-60          survival_3.5-5       mvtnorm_1.2-5        latticeExtra_0.6-30 
[13] lattice_0.21-8       hdf5r_1.3.11         Seurat_5.1.0         SeuratObject_5.0.2  
[17] sp_2.1-4             readxl_1.4.3         zoo_1.8-12           openxlsx_4.2.6.1    
[21] ggalluvial_0.12.5    plotly_4.10.4        gridExtra_2.3        ggplot2_3.5.1       
[25] dplyr_1.1.4          shinyFiles_0.9.3     shinydashboard_0.7.2 shinyjs_2.1.0       
[29] shiny_1.9.1         

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22            splines_4.3.1              
  [3] later_1.3.2                 bitops_1.0-8               
  [5] tibble_3.2.1                cellranger_1.1.0           
  [7] polyclip_1.10-7             rpart_4.1.19               
  [9] fastDummies_1.7.3           lifecycle_1.0.4            
 [11] globals_0.16.3              backports_1.5.0            
 [13] magrittr_2.0.3              vcd_1.4-12                 
 [15] sass_0.4.9                  Hmisc_5.1-3                
 [17] rmarkdown_2.27              jquerylib_0.1.4            
 [19] httpuv_1.6.15               spam_2.10-0                
 [21] zip_2.3.1                   spatstat.sparse_3.1-0      
 [23] reticulate_1.38.0           cowplot_1.1.3              
 [25] pbapply_1.7-2               RColorBrewer_1.1-3         
 [27] zlibbioc_1.48.2             abind_1.4-5                
 [29] GenomicRanges_1.54.1        Rtsne_0.17                 
 [31] purrr_1.0.2                 RCurl_1.98-1.16            
 [33] BiocGenerics_0.48.1         nnet_7.3-19                
 [35] sandwich_3.1-0              GenomeInfoDbData_1.2.11    
 [37] IRanges_2.36.0              S4Vectors_0.40.2           
 [39] ggrepel_0.9.5               irlba_2.3.5.1              
 [41] listenv_0.9.1               spatstat.utils_3.0-5       
 [43] goftest_1.2-3               RSpectra_0.16-2            
 [45] spatstat.random_3.3-1       fitdistrplus_1.2-1         
 [47] parallelly_1.38.0           DelayedArray_0.28.0        
 [49] leiden_0.4.3.1              codetools_0.2-19           
 [51] tidyselect_1.2.1            gmp_0.7-4                  
 [53] stats4_4.3.1                matrixStats_1.3.0          
 [55] base64enc_0.1-3             spatstat.explore_3.3-1     
 [57] jsonlite_1.8.8              progressr_0.14.0           
 [59] Formula_1.2-5               ggridges_0.5.6             
 [61] progress_1.2.3              tools_4.3.1                
 [63] ica_1.0-3                   Rcpp_1.0.13                
 [65] glue_1.7.0                  SparseArray_1.2.4          
 [67] xfun_0.46                   MatrixGenerics_1.14.0      
 [69] GenomeInfoDb_1.38.8         withr_3.0.1                
 [71] BiocManager_1.30.23         fastmap_1.2.0              
 [73] fansi_1.0.6                 digest_0.6.36              
 [75] R6_2.5.1                    mime_0.12                  
 [77] colorspace_2.1-1            scattermore_1.2            
 [79] tensor_1.5                  jpeg_0.1-10                
 [81] spatstat.data_3.1-2         utf8_1.2.4                 
 [83] tidyr_1.3.1                 generics_0.1.3             
 [85] renv_1.0.2                  data.table_1.15.4          
 [87] prettyunits_1.2.0           S4Arrays_1.2.1             
 [89] httr_1.4.7                  htmlwidgets_1.6.4          
 [91] uwot_0.2.2                  pkgconfig_2.0.3            
 [93] gtable_0.3.5                Rmpfr_0.9-5                
 [95] lmtest_0.9-40               XVector_0.42.0             
 [97] htmltools_0.5.8.1           dotCall64_1.1-1            
 [99] Biobase_2.62.0              scales_1.3.0               
[101] leaps_3.2                   png_0.1-8                  
[103] spatstat.univar_3.0-0       knitr_1.48                 
[105] rstudioapi_0.16.0           reshape2_1.4.4             
[107] checkmate_2.3.2             nlme_3.1-162               
[109] cachem_1.1.0                KernSmooth_2.23-21         
[111] parallel_4.3.1              miniUI_0.1.1.1             
[113] foreign_0.8-84              pillar_1.9.0               
[115] vctrs_0.6.5                 RANN_2.6.1                 
[117] promises_1.3.0              xtable_1.8-4               
[119] cluster_2.1.4               htmlTable_2.4.3            
[121] evaluate_0.24.0             cli_3.6.3                  
[123] compiler_4.3.1              crayon_1.5.3               
[125] rlang_1.1.4                 future.apply_1.11.2        
[127] interp_1.1-6                plyr_1.8.9                 
[129] fs_1.6.4                    stringi_1.8.4              
[131] viridisLite_0.4.2           deldir_2.0-4               
[133] munsell_0.5.1               lazyeval_0.2.2             
[135] spatstat.geom_3.3-2         Matrix_1.6-5               
[137] RcppHNSW_0.6.0              hms_1.1.3                  
[139] patchwork_1.2.0             bit64_4.0.5                
[141] future_1.34.0               SummarizedExperiment_1.32.0
[143] ROCR_1.0-11                 fontawesome_0.5.2          
[145] memoise_2.0.1               igraph_2.0.3               
[147] bslib_0.8.0                 bit_4.0.5  

[nick-youngblut]

By any chance, are you assuming that the user has Seurat v4 installed?

I don't see any version constraints (e.g., Seurat==4.1) in the repo.

[nick-youngblut]

If I load the GSE160729_SeuratObject.RDS object from Case 2, the object loads, but when I try to run QC, I get:

Warning: The `slot` argument of `GetAssayData()` is deprecated as of SeuratObject 5.0.0.
ℹ Please use the `layer` argument instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Warning: Layer counts isn't present in the assay object[[assay]]; returning NULL
Warning: Layer counts isn't present in the assay object[[assay]]; returning NULL
Warning: Layer counts isn't present in the assay object[[assay]]; returning NULL
Warning: Error in [[: ‘percent.mt’ not found in this Seurat object

So, it appears that this shiny app has not yet been updated for Seurat v5. Is that correct?