Error when using check_markers

[Gonzalo Soria Alcaide]

Hi all,

First of all, I recently found your tool in some Tcell annotation reviews and I loved the idea and the easy-to-follow workflow. Congratulations for the work, I'm really looking forward to apply it to my single-cell data and give it try.  Looks really good.

However, I'm encountering an error with the check_markers function. It seems to be related to the add_vertices function, but I am not sure why. This is the prompt message:

''''

marker_check <- check_markers(cds, marker_file_path,

                              db=get(ddbb),

                              cds_gene_id_type = "SYMBOL",

                              marker_file_gene_id_type = "SYMBOL",

                              use_tf_idf = FALSE)

There are 26 cell type definitions

Error in add_vertices(e1, la, attr = e2) : 

  At rinterface_extra.c:78 : Expecting a scalar integer but received a vector of length 2. Invalid value

''''

At first, I thought it might be a problem with the design of my markers.txt file, but I have already tried to use the one provided as reference for the PBMC model and the same error arises.

Also, my expression data comes from a seurat object (Im using the "counts" slot instead of the "data" as described in the documentation, as my seurat object is already normalized and clustered) . Just in case it might be a problem.

Below I leave my Rsession. I had some previous errors with version conflicts so It might be a thing (igraph wrong version ?)

Thanks in advance and sorry for any inconvenience.

Greetings,

G.

sessionInfo()

R version 4.3.2 (2023-10-31)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: macOS Big Sur ... 10.16

Matrix products: default

BLAS/LAPACK: /anaconda3/envs/seurat/lib/libopenblasp-r0.3.26.dylib;  LAPACK version 3.12.0

locale:

[1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8

time zone: Europe/Madrid

tzcode source: internal

attached base packages:

[1] splines   stats4    stats     graphics  grDevices utils     datasets 

[8] methods   base     

other attached packages:

 [1] org.Mm.eg.db_3.18.0  org.Hs.eg.db_3.18.0  AnnotationDbi_1.64.1

 [4] IRanges_2.36.0       S4Vectors_0.40.2     garnett_0.1.23      

 [7] monocle_2.30.0       DDRTree_0.1.5        irlba_2.3.5.1       

[10] VGAM_1.1-9           ggplot2_3.4.4        Biobase_2.62.0      

[13] BiocGenerics_0.48.1  Matrix_1.6-1.1      

loaded via a namespace (and not attached):

 [1] DBI_1.2.1                 bitops_1.0-7             

 [3] formatR_1.14              gridExtra_2.3            

 [5] rlang_1.1.3               magrittr_2.0.3           

 [7] matrixStats_1.2.0         compiler_4.3.2           

 [9] RSQLite_2.3.4             DelayedMatrixStats_1.24.0

[11] png_0.1-8                 systemfonts_1.0.5        

[13] vctrs_0.6.5               reshape2_1.4.4           

[15] combinat_0.0-8            stringr_1.5.1            

[17] pkgconfig_2.0.3           shape_1.4.6              

[19] crayon_1.5.2              fastmap_1.1.1            

[21] XVector_0.42.0            labeling_0.4.3           

[23] utf8_1.2.4                ragg_1.2.7               

[25] bit_4.0.5                 glmnet_4.1-8             

[27] zlibbioc_1.48.0           cachem_1.0.8             

[29] GenomeInfoDb_1.38.1       HSMMSingleCell_1.22.0    

[31] blob_1.2.4                DelayedArray_0.28.0      

[33] parallel_4.3.2            cluster_2.1.6            

[35] R6_2.5.1                  stringi_1.8.3            

[37] RColorBrewer_1.1-3        limma_3.58.1             

[39] Rcpp_1.0.12               assertthat_0.2.1         

[41] iterators_1.0.14          igraph_2.0.1.1           

[43] tidyselect_1.2.0          qlcMatrix_0.9.7          

[45] abind_1.4-5               viridis_0.6.5            

[47] codetools_0.2-19          docopt_0.7.1             

[49] lattice_0.22-5            tibble_3.2.1             

[51] plyr_1.8.9                withr_3.0.0              

[53] KEGGREST_1.42.0           Rtsne_0.17               

[55] lambda.r_1.2.4            survival_3.5-8           

[57] futile.logger_1.4.3       sparsesvd_0.2-2          

[59] Biostrings_2.70.1         pillar_1.9.0             

[61] MatrixGenerics_1.14.0     leidenbase_0.1.18        

[63] foreach_1.5.2             rly_1.7.4                

[65] generics_0.1.3            RCurl_1.98-1.14          

[67] sparseMatrixStats_1.14.0  munsell_0.5.0            

[69] scales_1.3.0              fastICA_1.2-4            

[71] glue_1.7.0                slam_0.1-50              

[73] pheatmap_1.0.12           tools_4.3.2              

[75] RANN_2.6.1                grid_4.3.2               

[77] colorspace_2.1-0          GenomeInfoDbData_1.2.11  

[79] cli_3.6.2                 textshaping_0.3.7        

[81] futile.options_1.0.1      fansi_1.0.6              

[83] S4Arrays_1.2.0            viridisLite_0.4.2        

[85] dplyr_1.1.4               gtable_0.3.4             

[87] SparseArray_1.2.2         farver_2.1.1             

[89] memoise_2.0.1             lifecycle_1.0.4          

[91] httr_1.4.7                statmod_1.5.0            

[93] bit64_4.0.5     

[hpl...@gmail.com]

Apologies for the very long delay. Were you able to run the example code in the documentation with the provided example data? (https://cole-trapnell-lab.github.io/garnett/docs/#checking-your-markers)