TIL Atlas reference atlas invalid

[Abnaveed]

Hey Thank you for your tool

I am trying to use the "ref_TILAtlas_mouse_v1.rds", but it keeps saying that the reference object is invalid and is giving me this error "Error in value[3L]". I can not import it as a Seurat object either

Here is my session info. Would appreciate any help

R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] dplyr_1.0.7        ProjecTILs_1.0.0   Matrix_1.3-4       TILPRED_1.0.2      umap_0.2.7.0       SeuratObject_4.0.2
[7] Seurat_4.0.4      

loaded via a namespace (and not attached):
  [1] nlme_3.1-153          matrixStats_0.61.0    spatstat.sparse_2.0-0 RcppAnnoy_0.0.19      RColorBrewer_1.1-2   
  [6] httr_1.4.2            sctransform_0.3.2     tools_4.1.1           utf8_1.2.2            R6_2.5.1             
 [11] irlba_2.3.3           rpart_4.1-15          KernSmooth_2.23-20    uwot_0.1.10           mgcv_1.8-37          
 [16] DBI_1.1.1             lazyeval_0.2.2        colorspace_2.0-2      tidyselect_1.1.1      gridExtra_2.3        
 [21] compiler_4.1.1        plotly_4.9.4.1        scales_1.1.1          lmtest_0.9-38         spatstat.data_2.1-0  
 [26] askpass_1.1           ggridges_0.5.3        pbapply_1.5-0         goftest_1.2-2         stringr_1.4.0        
 [31] digest_0.6.28         spatstat.utils_2.2-0  pkgconfig_2.0.3       htmltools_0.5.2       parallelly_1.28.1    
 [36] fastmap_1.1.0         htmlwidgets_1.5.4     rlang_0.4.11          shiny_1.7.1           generics_0.1.0       
 [41] zoo_1.8-9             jsonlite_1.7.2        ica_1.0-2             magrittr_2.0.1        patchwork_1.1.1      
 [46] Rcpp_1.0.7            munsell_0.5.0         fansi_0.5.0           abind_1.4-5           reticulate_1.22      
 [51] lifecycle_1.0.1       stringi_1.7.5         MASS_7.3-54           Rtsne_0.15            plyr_1.8.6           
 [56] grid_4.1.1            parallel_4.1.1        listenv_0.8.0         promises_1.2.0.1      ggrepel_0.9.1        
 [61] crayon_1.4.1          miniUI_0.1.1.1        deldir_1.0-2          lattice_0.20-45       cowplot_1.1.1        
 [66] splines_4.1.1         tensor_1.5            pillar_1.6.3          igraph_1.2.6          spatstat.geom_2.2-2  
 [71] future.apply_1.8.1    reshape2_1.4.4        codetools_0.2-18      leiden_0.3.9          glue_1.4.2           
 [76] data.table_1.14.2     BiocManager_1.30.16   png_0.1-7             vctrs_0.3.8           httpuv_1.6.3         
 [81] openssl_1.4.5         gtable_0.3.0          RANN_2.6.1            purrr_0.3.4           spatstat.core_2.3-0  
 [86] polyclip_1.10-0       tidyr_1.1.4           scattermore_0.7       future_1.22.1         assertthat_0.2.1     
 [91] ggplot2_3.3.5         mime_0.12             xtable_1.8-4          RSpectra_0.16-0       later_1.3.0          
 [96] survival_3.2-13       viridisLite_0.4.0     tibble_3.1.5          cluster_2.1.2         globals_0.14.0       
[101] fitdistrplus_1.1-6    ellipsis_0.3.2        ROCR_1.0-11 

[mass-a]

Hello!

my guess is that the reference object didn't download correctly. Can you try to delete it and download it again? If the download through R times out (as sometimes happens), you can get the object directly from https://doi.org/10.6084/m9.figshare.12478571

Let us know if the problem persists.

[Abnaveed]

Hey

Yeah whenever I try downloading it through R, it says the download is complete but then the object is not usable. I downloaded it directly from the link. Its working perfectly. Thank You