Error in keepHighGene(raw_ts_data, verbose = verbose) : no slot of name "meta.data" for this object of class "Assay"

[Urology-weiyu]

Error in keepHighGene(raw_ts_data, verbose = verbose) : no slot of name "meta.data" for this object of class "Assay"

[zijianni]

Hi @Urology-weiyu , thanks for reporting your issue. Can you attach the session info? The code you are running seems pretty standard. Suspecting it's due to outdated package versions.

[Urology-weiyu]

Thank you for your prompt reply, and my session info was as following:

R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

Matrix products: default


locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8  LC_CTYPE=Chinese (Simplified)_China.utf8    LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                                LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] S4Vectors_0.38.1   SeuratObject_5.0.0 Seurat_4.4.0       SpotClean_1.4.1   

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3          rstudioapi_0.15.0           jsonlite_1.8.7              magrittr_2.0.3              magick_2.8.1                spatstat.utils_3.0-4       
  [7] zlibbioc_1.40.0             fs_1.6.3                    vctrs_0.6.3                 ROCR_1.0-11                 memoise_2.0.1               spatstat.explore_3.2-5     
 [13] RCurl_1.98-1.12             bmp_0.3                     S4Arrays_1.2.0              htmltools_0.5.6.1           usethis_2.2.2               readbitmap_0.1.5           
 [19] Rhdf5lib_1.24.0             rhdf5_2.46.0                SparseArray_1.2.0           sctransform_0.4.1           parallelly_1.36.0           KernSmooth_2.23-22         
 [25] htmlwidgets_1.6.2           ica_1.0-3                   plyr_1.8.8                  plotly_4.10.3               zoo_1.8-12                  cachem_1.0.8               
 [31] igraph_1.5.1                mime_0.12                   lifecycle_1.0.3             pkgconfig_2.0.3             Matrix_1.6-1                R6_2.5.1                   
 [37] fastmap_1.1.1               GenomeInfoDbData_1.2.11     MatrixGenerics_1.14.0       fitdistrplus_1.1-11         future_1.33.0               shiny_1.7.5.1              
 [43] digest_0.6.33               colorspace_2.1-0            patchwork_1.1.3             ps_1.7.5                    tensor_1.5                  irlba_2.3.5.1              
 [49] pkgload_1.3.3               GenomicRanges_1.54.1        progressr_0.14.0            fansi_1.0.4                 spatstat.sparse_3.0-3       httr_1.4.7                 
 [55] polyclip_1.10-4             abind_1.4-5                 compiler_4.3.1              remotes_2.4.2.1             withr_2.5.2                 tiff_0.1-12                
 [61] viridis_0.6.4               pkgbuild_1.4.2              MASS_7.3-60                 DelayedArray_0.28.0         sessioninfo_1.2.2           rjson_0.2.21               
 [67] tools_4.3.1                 lmtest_0.9-40               httpuv_1.6.12               future.apply_1.11.0         goftest_1.2-3               glue_1.6.2                 
 [73] callr_3.7.3                 rhdf5filters_1.14.0         nlme_3.1-163                promises_1.2.1              grid_4.3.1                  Rtsne_0.16                 
 [79] cluster_2.1.4               reshape2_1.4.4              generics_0.1.3              gtable_0.3.4                spatstat.data_3.0-3         tidyr_1.3.0                
 [85] data.table_1.14.8           XVector_0.34.0              sp_2.1-1                    utf8_1.2.3                  BiocGenerics_0.48.0         spatstat.geom_3.2-7        
 [91] RcppAnnoy_0.0.21            ggrepel_0.9.3               RANN_2.6.1                  pillar_1.9.0                stringr_1.5.0               spam_2.10-0                
 [97] later_1.3.1                 splines_4.3.1               dplyr_1.1.3                 lattice_0.21-8              survival_3.5-7              deldir_1.0-9               
[103] tidyselect_1.2.0            SingleCellExperiment_1.24.0 miniUI_0.1.1.1              pbapply_1.7-2               gridExtra_2.3               IRanges_2.36.0             
[109] SummarizedExperiment_1.32.0 scattermore_1.2             stats4_4.3.1                Biobase_2.54.0              devtools_2.4.5              matrixStats_1.0.0          
[115] stringi_1.7.12              lazyeval_0.2.2              codetools_0.2-19            tibble_3.2.1                cli_3.6.1                   uwot_0.1.16                
[121] xtable_1.8-4                reticulate_1.34.0           munsell_0.5.0               processx_3.8.2              GenomeInfoDb_1.38.0         Rcpp_1.0.11                
[127] globals_0.16.2              spatstat.random_3.2-1       png_0.1-8                   parallel_4.3.1              ellipsis_0.3.2              ggh4x_0.2.6                
[133] ggplot2_3.4.4               prettyunits_1.2.0           dotCall64_1.1-0             jpeg_0.1-10                 profvis_0.3.8               urlchecker_1.0.1           
[139] bitops_1.0-7                listenv_0.9.0               SpatialExperiment_1.12.0    viridisLite_0.4.2           scales_1.2.1                ggridges_0.5.4             
[145] leiden_0.4.3                purrr_1.0.2                 crayon_1.5.2                rlang_1.1.1                 cowplot_1.1.1

Here i noticed that the SpotClean was built on R 4.3.2, was it possible the cause of error?

[Urology-weiyu]

And in addition, the whole view of resutls was:

> rawdata=read10xRawH5('PATH/TO/raw_feature_bc_matrix.h5')
> spatial_dir='PATH/TO/spatial'
> slide_info <- read10xSlide(tissue_csv_file=file.path(spatial_dir,
>                                                             "tissue_positions_list.csv"),
>                                   tissue_img_file = file.path(spatial_dir,
>                                                               "tissue_lowres_image.png"),
>                                   scale_factor_file = file.path(spatial_dir,
>                                                                 "scalefactors_json.json"))
> slide_obj <- createSlide(rawdata, slide_info)

Filtered out 30483 genes with average expressions below or equal to 0.1.

> decont_obj <- spotclean(slide_obj);

2024-01-05 22:08:26.854417 Start.
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
Error in keepHighGene(raw_ts_data, verbose = verbose) : 
  no slot of name "meta.data" for this object of class "Assay"

[Urology-weiyu]

In my last attempt with R 4.3.2 and newly installed packages, it went successfully. Thank you for your work.

[zijianni]

Glad you've figured it out - there has been some major updates to Seurat and related packages so it might be incompatible with older versions.