RunICA error - DimReduc” object: rownames must be present in 'cell.embeddings

[daniel-spies]

I do encounter the following error after importing 10X spatial h5 object when performing the RunICA function:

Error in validObject(.Object) : invalid class “DimReduc” object: rownames must be present in 'cell.embeddings'

Data was read using the Load10X_Spatial function. The SeuratDisk library was installed and loaded as well as the SeuratData::UpdateSeuratObject did not resolve the error, thus I exclude issues do to saving/loading the file from different Seurat versions.

Debugging the function get to the point where CreateDimReducObject is called, so it really seems that due to a change in conformity checks causes this error.

while the colnames are set in RunICA.default for both cell.embeddings and feature.loadings the rownames are not.

R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS 14.5

Matrix products: default
LAPACK: /Users/spies.daniel/opt/miniconda3/lib/libopenblasp-r0.3.27.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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] dplyr_1.1.4           SeuratDisk_0.0.0.9021 ggplot2_3.5.1         patchwork_1.2.0       SeuratData_0.2.2.9001 Seurat_5.0.1          SeuratObject_5.0.1    sp_1.5-1              BiocManager_1.30.23  

loaded via a namespace (and not attached):
  [1] Rtsne_0.16                  colorspace_2.0-3            deldir_1.0-6                ggridges_0.5.6              XVector_0.34.0              GenomicRanges_1.46.1        RcppHNSW_0.4.1              spatstat.data_3.0-0        
  [9] farver_2.1.1                leiden_0.4.3.1              listenv_0.9.1               bit64_4.0.5                 ggrepel_0.9.5               RSpectra_0.16-1             fansi_1.0.3                 sparseMatrixStats_1.6.0    
 [17] codetools_0.2-20            splines_4.1.3               polyclip_1.10-4             pkgload_1.3.4               spam_2.9-1                  jsonlite_1.8.3              ica_1.0-3                   cluster_2.1.4              
 [25] png_0.1-7                   uwot_0.1.14                 shiny_1.8.1.1               sctransform_0.4.1           spatstat.sparse_3.0-0       compiler_4.1.3              httr_1.4.7                  Matrix_1.6-4               
 [33] fastmap_1.1.1               lazyeval_0.2.2              cli_3.6.3                   later_1.3.0                 htmltools_0.5.8.1           tools_4.1.3                 igraph_2.0.3                dotCall64_1.0-2            
 [41] GenomeInfoDbData_1.2.7      gtable_0.3.5                glue_1.6.2                  RANN_2.6.1                  reshape2_1.4.4              rappdirs_0.3.3              Rcpp_1.0.9                  Biobase_2.54.0             
 [49] scattermore_1.2             vctrs_0.6.5                 spatstat.explore_3.0-5      nlme_3.1-160                progressr_0.14.0            DelayedMatrixStats_1.16.0   lmtest_0.9-40               spatstat.random_3.0-1      
 [57] stringr_1.5.1               globals_0.16.3              mime_0.12                   miniUI_0.1.1.1              lifecycle_1.0.4             irlba_2.3.5.1               goftest_1.2-3               future_1.29.0              
 [65] zlibbioc_1.40.0             MASS_7.3-58.1               zoo_1.8-11                  scales_1.3.0                MatrixGenerics_1.6.0        promises_1.2.0.1            spatstat.utils_3.0-1        SummarizedExperiment_1.24.0
 [73] parallel_4.1.3              RColorBrewer_1.1-3          reticulate_1.26             pbapply_1.7-2               gridExtra_2.3               stringi_1.7.8               S4Vectors_0.32.4            fastDummies_1.7.3          
 [81] BiocGenerics_0.40.0         GenomeInfoDb_1.30.1         bitops_1.0-7                rlang_1.1.4                 pkgconfig_2.0.3             matrixStats_0.63.0          glmGamPoi_1.6.0             lattice_0.20-45            
 [89] ROCR_1.0-11                 purrr_1.0.2                 tensor_1.5                  labeling_0.4.3              htmlwidgets_1.6.4           bit_4.0.5                   cowplot_1.1.3               tidyselect_1.2.1           
 [97] parallelly_1.32.1           RcppAnnoy_0.0.20            plyr_1.8.8                  magrittr_2.0.3              R6_2.5.1                    IRanges_2.28.0              generics_0.1.3              DelayedArray_0.20.0        
[105] DBI_1.2.3                   pillar_1.9.0                withr_3.0.0                 fitdistrplus_1.1-11         RCurl_1.98-1.9              survival_3.4-0              abind_1.4-5                 tibble_3.2.1               
[113] future.apply_1.11.2         hdf5r_1.3.7                 crayon_1.5.3                KernSmooth_2.23-20          utf8_1.2.2                  spatstat.geom_3.0-3         plotly_4.10.4               grid_4.1.3                 
[121] data.table_1.14.6           digest_0.6.30               xtable_1.8-4                tidyr_1.3.1                 httpuv_1.6.6                stats4_4.1.3                munsell_0.5.1               viridisLite_0.4.2 ```