Velocyto- Seurat - invalid class “LogMap” object: Duplicate rownames not allowed

[Ruba-Mahmoud]

Hello, first thank you for developing such great tools I am Ruba PhD student in Germany and I am doing scRNAseq analysis for my data, I wanted to check the velocity and so I generated the loom files by velacyto, I wanted to continue with Seurat with .r but unfortunately am facing some errors, I looked many published errors, tried to downgrade the Matrix Package (where Seurat didn't work anymore) I had to upgrade it again, the error am facing is | | 0%Error in validObject(.Object) : invalid class “LogMap” object: Duplicate rownames not allowed taking into account there's no duplicated rownames could somebody kindly look into it and give an advice if something could be done so I can go through the velocity analysis in the end.

thank you in advance

Kind regards!

library(Seurat)
library(SeuratWrappers)
library(velocyto.R)
library(Matrix)

ldat <- ReadVelocity(file = "E11.5.possorted_genome_bam_BX5BE.loom")
Seurat::bm <- as.Seurat(x= ldat)

output

  |                                                                                                                                          |   0%Error in validObject(.Object) : 
  invalid class “LogMap” object: Duplicate rownames not allowed 

any(duplicated(rownames(ldat)))
[1] FALSE

> class(ldat)
[1] "list"

> str(ldat)
List of 3
 $ spliced  :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. ..@ i       : int [1:12963443] 100 110 111 177 263 376 461 467 472 500 ...
  .. ..@ p       : int [1:14699] 0 679 1555 2345 3484 3870 5098 6066 7591 8934 ...
  .. ..@ Dim     : int [1:2] 32285 14698
  .. ..@ Dimnames:List of 2
  .. .. ..$ : chr [1:32285] "AC125149.3" "AC125149.5" "AC125149.2" "AC125149.1" ...
  .. .. ..$ : chr [1:14698] "possorted_genome_bam_BX5BE:AAAGCAACAGGTCGTCx" "possorted_genome_bam_BX5BE:AAAGCAATCTGCGTAAx" "possorted_genome_bam_BX5BE:AAACGGGCAGATGAGCx" "possorted_genome_bam_BX5BE:AAAGCAAGTACAGTTCx" ...
  .. ..@ x       : num [1:12963443] 1 2 1 1 1 1 1 1 2 1 ...
  .. ..@ factors : list()
 $ unspliced:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. ..@ i       : int [1:7903683] 195 411 501 526 548 586 615 723 851 985 ...
  .. ..@ p       : int [1:14699] 0 309 579 864 1999 2017 2490 2712 4181 4807 ...
  .. ..@ Dim     : int [1:2] 32285 14698
  .. ..@ Dimnames:List of 2
  .. .. ..$ : chr [1:32285] "AC125149.3" "AC125149.5" "AC125149.2" "AC125149.1" ...
  .. .. ..$ : chr [1:14698] "possorted_genome_bam_BX5BE:AAAGCAACAGGTCGTCx" "possorted_genome_bam_BX5BE:AAAGCAATCTGCGTAAx" "possorted_genome_bam_BX5BE:AAACGGGCAGATGAGCx" "possorted_genome_bam_BX5BE:AAAGCAAGTACAGTTCx" ...
  .. ..@ x       : num [1:7903683] 2 3 2 1 1 1 3 1 1 1 ...
  .. ..@ factors : list()
 $ ambiguous:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. ..@ i       : int [1:1881126] 214 274 615 738 783 867 1469 2097 2828 2954 ...
  .. ..@ p       : int [1:14699] 0 85 160 245 453 481 617 714 1038 1231 ...
  .. ..@ Dim     : int [1:2] 32285 14698
  .. ..@ Dimnames:List of 2
  .. .. ..$ : chr [1:32285] "AC125149.3" "AC125149.5" "AC125149.2" "AC125149.1" ...
  .. .. ..$ : chr [1:14698] "possorted_genome_bam_BX5BE:AAAGCAACAGGTCGTCx" "possorted_genome_bam_BX5BE:AAAGCAATCTGCGTAAx" "possorted_genome_bam_BX5BE:AAACGGGCAGATGAGCx" "possorted_genome_bam_BX5BE:AAAGCAAGTACAGTTCx" ...
  .. ..@ x       : num [1:1881126] 1 1 1 1 1 2 1 1 1 1 ...
  .. ..@ factors : list()

> sessionInfo()
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

time zone: Europe/Berlin
tzcode source: internal

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

other attached packages:
[1] velocyto.R_0.6       Matrix_1.6-4         SeuratWrappers_0.3.2 Seurat_5.0.1         SeuratObject_5.0.1   sp_2.1-2            

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3     rstudioapi_0.15.0      jsonlite_1.8.8         magrittr_2.0.3         spatstat.utils_3.0-4   fs_1.6.3              
  [7] vctrs_0.6.4            ROCR_1.0-11            memoise_2.0.1          spatstat.explore_3.2-5 htmltools_0.5.7        usethis_2.2.2         
 [13] sctransform_0.4.1      parallelly_1.36.0      KernSmooth_2.23-22     htmlwidgets_1.6.4      ica_1.0-3              plyr_1.8.9            
 [19] plotly_4.10.3          zoo_1.8-12             cachem_1.0.8           igraph_1.6.0           mime_0.12              lifecycle_1.0.4       
 [25] pkgconfig_2.0.3        rsvd_1.0.5             R6_2.5.1               fastmap_1.1.1          fitdistrplus_1.1-11    future_1.33.1         
 [31] shiny_1.8.0            digest_0.6.33          pcaMethods_1.92.0      colorspace_2.1-0       patchwork_1.2.0        tensor_1.5            
 [37] RSpectra_0.16-1        irlba_2.3.5.1          pkgload_1.3.3          progressr_0.14.0       fansi_1.0.6            spatstat.sparse_3.0-3 
 [43] httr_1.4.7             polyclip_1.10-6        abind_1.4-5            mgcv_1.9-0             compiler_4.3.2         remotes_2.4.2.1       
 [49] bit64_4.0.5            fastDummies_1.7.3      pkgbuild_1.4.3         R.utils_2.12.3         MASS_7.3-60            sessioninfo_1.2.2     
 [55] tools_4.3.2            lmtest_0.9-40          httpuv_1.6.12          future.apply_1.11.1    goftest_1.2-3          R.oo_1.25.0           
 [61] glue_1.6.2             nlme_3.1-163           promises_1.2.1         grid_4.3.2             Rtsne_0.17             cluster_2.1.4         
 [67] reshape2_1.4.4         generics_0.1.3         hdf5r_1.3.8            gtable_0.3.4           spatstat.data_3.0-3    R.methodsS3_1.8.2     
 [73] tidyr_1.3.0            data.table_1.14.10     utf8_1.2.4             BiocGenerics_0.48.1    spatstat.geom_3.2-7    RcppAnnoy_0.0.21      
 [79] ggrepel_0.9.5          RANN_2.6.1             pillar_1.9.0           stringr_1.5.1          spam_2.10-0            RcppHNSW_0.5.0        
 [85] later_1.3.1            splines_4.3.2          dplyr_1.1.4            lattice_0.21-9         bit_4.0.5              survival_3.5-7        
 [91] deldir_2.0-2           tidyselect_1.2.0       miniUI_0.1.1.1         pbapply_1.7-2          gridExtra_2.3          scattermore_1.2       
 [97] Biobase_2.62.0         devtools_2.4.5         matrixStats_1.2.0      stringi_1.8.3          lazyeval_0.2.2         codetools_0.2-19      
[103] tibble_3.2.1           BiocManager_1.30.22    cli_3.6.1              uwot_0.1.16            xtable_1.8-4           reticulate_1.34.0     
[109] munsell_0.5.0          Rcpp_1.0.11            globals_0.16.2         spatstat.random_3.2-2  png_0.1-8              parallel_4.3.2        
[115] ellipsis_0.3.2         ggplot2_3.4.4          dotCall64_1.1-1        profvis_0.3.8          urlchecker_1.0.1       listenv_0.9.0         
[121] viridisLite_0.4.2      scales_1.3.0           ggridges_0.5.5         leiden_0.4.3.1         purrr_1.0.2            rlang_1.1.2           
[127] cowplot_1.1.2

[fariznazir]

Hi, please check for duplicate column names in the infercnv object's expression and the counts matrix. If you do, then getting rid of them will help. I was running CNV analysis and had to remove duplicate column names to get rid of the error.

[xgqyoung]

Hi. I got the same error, have you solved yet?

[jwtobias]

Also hoping for a solution.

[hwick]

in the infercnv object's expression

@fariznazir Can you clarify what you mean? The person who originally made this issue does not have an object called infercnv. The error refers to rownames. Is invercnv part of the loom file? are colnames converted to rownames at some point?