Errors in CellTrek::traint on example data from README

[katherine-benjamin]

I'm attempting to get the example from the README working, but am encountering an error on the CellTrek::traint step during FindTransferAnchors:

> brain_traint <- CellTrek::traint(st_data=brain_st_cortex, sc_data=brain_sc, sc_assay='RNA', cell_names='cell_type')
Finding transfer anchors... 
Using 2000 features for integration... 
Running CCA
Merging objects
Error in dimnames(x) <- dn : 
  length of 'dimnames' [1] not equal to array extent
In addition: Warning messages:
1: Command ScaleData.RNA changing from SeuratCommand to SeuratCommand 
2: Command ScaleData.Spatial changing from SeuratCommand to SeuratCommand 
3: In RunCCA.Seurat(object1 = reference, object2 = query, features = features,  :
  Running CCA on different assays

Downgrading to Seurat 3.1.1 (corresponding to Version(brain_sc)) gets us past this step but encounters a new error slightly later in the execution of FindTransferAnchors. I've included that error at the end of this issue in case it is useful.

---

Debugging info (Seurat 4.4.0)

Traceback

> traceback()
5: `rownames<-`(x = `*tmp*`, value = Cells(x = combined.object))
4: RunCCA.Seurat(object1 = reference, object2 = query, features = features, 
       num.cc = max(dims), renormalize = FALSE, rescale = FALSE, 
       verbose = verbose)
3: RunCCA(object1 = reference, object2 = query, features = features, 
       num.cc = max(dims), renormalize = FALSE, rescale = FALSE, 
       verbose = verbose)
2: Seurat::FindTransferAnchors(reference = sc_data, query = st_data, 
       reference.assay = sc_assay, query.assay = st_assay, normalization.method = norm, 
       features = sc_st_features, reduction = "cca", ...)
1: CellTrek::traint(st_data = brain_st_cortex, sc_data = brain_sc, 
       sc_assay = "RNA", cell_names = "cell_type")

Session Info

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1

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: Europe/London
tzcode source: internal

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

other attached packages:
[1] viridis_0.6.4      viridisLite_0.4.2  dplyr_1.1.3        SeuratObject_5.0.0
[5] Seurat_4.4.0       CellTrek_0.0.94   

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3     rstudioapi_0.15.0      jsonlite_1.8.7        
  [4] magrittr_2.0.3         spatstat.utils_3.0-3   farver_2.1.1          
  [7] vctrs_0.6.3            ROCR_1.0-11            spatstat.explore_3.2-3
 [10] rstatix_0.7.2          htmltools_0.5.6        dynamicTreeCut_1.63-1 
 [13] broom_1.0.5            sctransform_0.4.0      parallelly_1.36.0     
 [16] KernSmooth_2.23-20     htmlwidgets_1.6.2      ica_1.0-3             
 [19] plyr_1.8.8             plotly_4.10.2          zoo_1.8-12            
 [22] igraph_1.5.1           mime_0.12              lifecycle_1.0.3       
 [25] pkgconfig_2.0.3        Matrix_1.6-1.1         R6_2.5.1              
 [28] fastmap_1.1.1          magic_1.6-1            fitdistrplus_1.1-11   
 [31] future_1.33.0          shiny_1.7.5            digest_0.6.33         
 [34] colorspace_2.1-0       patchwork_1.1.3        tensor_1.5            
 [37] irlba_2.3.5.1          akima_0.6-3.4          ggpubr_0.6.0          
 [40] labeling_0.4.3         philentropy_0.7.0      progressr_0.14.0      
 [43] fansi_1.0.4            spatstat.sparse_3.0-2  httr_1.4.7            
 [46] polyclip_1.10-4        abind_1.4-5            compiler_4.3.0        
 [49] withr_2.5.0            backports_1.4.1        carData_3.0-5         
 [52] ggsignif_0.6.4         MASS_7.3-58.4          tools_4.3.0           
 [55] lmtest_0.9-40          httpuv_1.6.11          future.apply_1.11.0   
 [58] goftest_1.2-3          glue_1.6.2             dbscan_1.1-11         
 [61] DiagrammeR_1.0.10      nlme_3.1-162           promises_1.2.1        
 [64] grid_4.3.0             Rtsne_0.16             cluster_2.1.4         
 [67] reshape2_1.4.4         generics_0.1.3         gtable_0.3.4          
 [70] spatstat.data_3.0-1    tidyr_1.3.0            data.table_1.14.8     
 [73] sp_2.0-0               car_3.1-2              utf8_1.2.3            
 [76] spatstat.geom_3.2-5    RcppAnnoy_0.0.21       ggrepel_0.9.3         
 [79] RANN_2.6.1             pillar_1.9.0           stringr_1.5.0         
 [82] spam_2.10-0            later_1.3.1            splines_4.3.0         
 [85] lattice_0.21-8         survival_3.5-5         deldir_1.0-9          
 [88] tidyselect_1.2.0       miniUI_0.1.1.1         pbapply_1.7-2         
 [91] gridExtra_2.3          scattermore_1.2        matrixStats_1.0.0     
 [94] visNetwork_2.1.2       stringi_1.7.12         lazyeval_0.2.2        
 [97] codetools_0.2-19       data.tree_1.0.0        tibble_3.2.1          
[100] packcircles_0.3.6      cli_3.6.1              uwot_0.1.16           
[103] xtable_1.8-4           geometry_0.4.7         reticulate_1.32.0     
[106] randomForestSRC_3.2.2  munsell_0.5.0          Rcpp_1.0.11           
[109] globals_0.16.2         spatstat.random_3.1-6  png_0.1-8             
[112] fastcluster_1.2.3      parallel_4.3.0         ellipsis_0.3.2        
[115] ggplot2_3.4.3          dotCall64_1.1-0        listenv_0.9.0         
[118] scales_1.2.1           ggridges_0.5.4         leiden_0.4.3          
[121] purrr_1.0.2            rlang_1.1.1            cowplot_1.1.1    

---

Debugging info (Seurat 3.1.1)

Error

> brain_traint <- CellTrek::traint(st_data=brain_st_cortex, sc_data=brain_sc, sc_assay='RNA', cell_names='cell_type')
Finding transfer anchors... 
Using 2000 features for integration... 
Running CCA
Merging objects
Finding neighborhoods
Finding anchors
Error in !(cells1 %in% colnames(object)) || !(cells2 %in% colnames(object)) : 
  'length = 5860' in coercion to 'logical(1)'
In addition: Warning message:
In RunCCA.Seurat(object1 = reference, object2 = query, features = features,  :
  Running CCA on different assays

Traceback

> traceback()
4: FindAnchorPairs(object = object.pair, integration.name = "integrated", 
       k.anchor = k.anchor, verbose = verbose)
3: FindAnchors(object.pair = combined.ob, assay = c(reference.assay, 
       query.assay), slot = slot, cells1 = colnames(x = reference), 
       cells2 = colnames(x = query), reduction = reduction, internal.neighbors = list(NULL, 
           NULL), dims = dims, k.anchor = k.anchor, k.filter = k.filter, 
       k.score = k.score, max.features = max.features, nn.method = nn.method, 
       eps = eps, projected = projected, verbose = verbose)
2: Seurat::FindTransferAnchors(reference = sc_data, query = st_data, 
       reference.assay = sc_assay, query.assay = st_assay, normalization.method = norm, 
       features = sc_st_features, reduction = "cca", ...)
1: CellTrek::traint(st_data = brain_st_cortex, sc_data = brain_sc, 
       sc_assay = "RNA", cell_names = "cell_type")

Session Info

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1

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: Europe/London
tzcode source: internal

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

other attached packages:
[1] CellTrek_0.0.94 Seurat_3.1.1   

loaded via a namespace (and not attached):
  [1] mathjaxr_1.6-0        RColorBrewer_1.1-3    rstudioapi_0.15.0    
  [4] jsonlite_1.8.7        magrittr_2.0.3        TH.data_1.1-2        
  [7] vctrs_0.6.3           multtest_2.8.0        ROCR_1.0-11          
 [10] rstatix_0.7.2         htmltools_0.5.6       dynamicTreeCut_1.63-1
 [13] plotrix_3.8-2         broom_1.0.5           sctransform_0.4.0    
 [16] parallelly_1.36.0     KernSmooth_2.23-20    htmlwidgets_1.6.2    
 [19] ica_1.0-3             plyr_1.8.8            sandwich_3.0-2       
 [22] plotly_4.10.2         zoo_1.8-12            igraph_1.5.1         
 [25] mime_0.12             lifecycle_1.0.3       pkgconfig_2.0.3      
 [28] rsvd_1.0.5            Matrix_1.6-1.1        R6_2.5.1             
 [31] fastmap_1.1.1         magic_1.6-1           rbibutils_2.2.16     
 [34] fitdistrplus_1.1-11   future_1.33.0         shiny_1.7.5          
 [37] digest_0.6.33         numDeriv_2016.8-1.1   colorspace_2.1-0     
 [40] irlba_2.3.5.1         akima_0.6-3.4         ggpubr_0.6.0         
 [43] philentropy_0.7.0     fansi_1.0.4           httr_1.4.7           
 [46] TFisher_0.2.0         abind_1.4-5           compiler_4.3.0       
 [49] mutoss_0.1-13         backports_1.4.1       carData_3.0-5        
 [52] R.utils_2.12.2        ggsignif_0.6.4        MASS_7.3-58.4        
 [55] tsne_0.1-3.1          tools_4.3.0           lmtest_0.9-40        
 [58] ape_5.7-1             metap_1.9             httpuv_1.6.11        
 [61] future.apply_1.11.0   qqconf_1.3.2          R.oo_1.25.0          
 [64] glue_1.6.2            dbscan_1.1-11         DiagrammeR_1.0.10    
 [67] promises_1.2.1        nlme_3.1-162          grid_4.3.0           
 [70] Rtsne_0.16            cluster_2.1.4         reshape2_1.4.4       
 [73] generics_0.1.3        gtable_0.3.4          R.methodsS3_1.8.2    
 [76] tidyr_1.3.0           sn_2.1.1              data.table_1.14.8    
 [79] sp_2.0-0              car_3.1-2             utf8_1.2.3           
 [82] BiocGenerics_0.48.0   RcppAnnoy_0.0.21      ggrepel_0.9.3        
 [85] RANN_2.6.1            pillar_1.9.0          stringr_1.5.0        
 [88] later_1.3.1           splines_4.3.0         dplyr_1.1.3          
 [91] lattice_0.21-8        survival_3.5-5        tidyselect_1.2.0     
 [94] pbapply_1.7-2         gridExtra_2.3         stats4_4.3.0         
 [97] Biobase_2.62.0        matrixStats_1.0.0     visNetwork_2.1.2     
[100] stringi_1.7.12        lazyeval_0.2.2        codetools_0.2-19     
[103] data.tree_1.0.0       tibble_3.2.1          packcircles_0.3.6    
[106] cli_3.6.1             uwot_0.1.16           geometry_0.4.7       
[109] xtable_1.8-4          reticulate_1.32.0     randomForestSRC_3.2.2
[112] Rdpack_2.5            munsell_0.5.0         Rcpp_1.0.11          
[115] globals_0.16.2        png_0.1-8             fastcluster_1.2.3    
[118] parallel_4.3.0        ellipsis_0.3.2        ggplot2_3.4.3        
[121] listenv_0.9.0         viridisLite_0.4.2     mvtnorm_1.2-3        
[124] SDMTools_1.1-221      scales_1.2.1          ggridges_0.5.4       
[127] leiden_0.4.3          purrr_1.0.2           rlang_1.1.1          
[130] cowplot_1.1.1         multcomp_1.4-25       mnormt_2.1.1  

[DingtaoHu]

I am facing the same questuion, have you solved this error? Could downgrading the Seurat version solve this problem?

[shiyuzhang98]

same question here, any solution now?

[williamhsy]

Same error here. May be related to the Seruat verison. After changing Seurat to version 4.3.0 and SeuratObject to version 4.1.4, it works.

[suanzaoren]

Same error here. May be related to the Seruat verison. After changing Seurat to version 4.3.0 and SeuratObject to version 4.1.4, it works.

That's wonderful!
And the SeuratObject download link is https://github.com/satijalab/seurat-object/archive/refs/tags/v4.1.4.tar.gz ,then install it locally.
The download code of Seurat is remotes::install_version("Seurat", "4.3.0", repos = c("https://satijalab.r-universe.dev", getOption("repos")))