performNormalization: Error in t.default(enrichment) : argument is not a matrix

[toobiwankenobi]

Hi @ncborcherding ,

This is more of an FYI than an issue.

After running runEscape(), I was trying to normalize the data with performNormalization(). I'm getting this error message: Error in t.default(enrichment) : argument is not a matrix. I checked the escape assay with its data layer.

class(acinarEscape@assays$escape$data)
[1] "dgCMatrix"
attr(,"package")
[1] "Matrix"

After changing the class of the layer, the normalization works.

acinarEscape@assays$escape$data <- as.matrix(acinarEscape@assays$escape$data)

The class dgCMatrix was assigned by Seurat. So I guess this format should be supported by escape.

Best wishes,
Tobi

> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.3.2

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

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/Zurich
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Matrix_1.7-3         GSEABase_1.68.0      graph_1.84.1         annotate_1.84.0      XML_3.99-0.18        AnnotationDbi_1.68.0 IRanges_2.40.1      
 [8] S4Vectors_0.44.0     Biobase_2.66.0       BiocGenerics_0.52.0  BiocParallel_1.40.2  gridExtra_2.3        msigdbr_24.1.0       escape_2.5.0        
[15] tidyr_1.3.1          rstatix_0.7.2        ggpubr_0.6.0         ggbeeswarm_0.7.2     ggplot2_3.5.2        stringr_1.5.1        dplyr_1.1.4         
[22] reticulate_1.42.0    Seurat_5.3.0         SeuratObject_5.1.0   sp_2.2-0            

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22            splines_4.4.2               later_1.4.2                 R.oo_1.27.1                 tibble_3.2.1               
  [6] polyclip_1.10-7             fastDummies_1.7.5           lifecycle_1.0.4             globals_0.18.0              lattice_0.22-7             
 [11] MASS_7.3-65                 ggdist_3.3.3                backports_1.5.0             magrittr_2.0.3              limma_3.62.2               
 [16] plotly_4.10.4               rmarkdown_2.29              yaml_2.3.10                 httpuv_1.6.16               sctransform_0.4.2          
 [21] spam_2.11-1                 spatstat.sparse_3.1-0       DBI_1.2.3                   cowplot_1.1.3               pbapply_1.7-2              
 [26] RColorBrewer_1.1-3          abind_1.4-8                 pkgload_1.4.0               zlibbioc_1.52.0             Rtsne_0.17                 
 [31] GenomicRanges_1.58.0        R.utils_2.13.0              purrr_1.0.4                 GenomeInfoDbData_1.2.13     ggrepel_0.9.6              
 [36] irlba_2.3.5.1               listenv_0.9.1               spatstat.utils_3.1-4        GSVA_2.0.7                  goftest_1.2-3              
 [41] RSpectra_0.16-2             spatstat.random_3.4-1       fitdistrplus_1.2-2          parallelly_1.44.0           DelayedMatrixStats_1.28.1  
 [46] codetools_0.2-20            DelayedArray_0.32.0         tidyselect_1.2.1            UCSC.utils_1.2.0            farver_2.1.2               
 [51] ScaledMatrix_1.14.0         matrixStats_1.5.0           spatstat.explore_3.4-3      jsonlite_2.0.0              progressr_0.15.1           
 [56] Formula_1.2-5               ggridges_0.5.6              survival_3.8-3              tools_4.4.2                 ica_1.0-3                  
 [61] Rcpp_1.0.14                 glue_1.8.0                  BiocBaseUtils_1.8.0         SparseArray_1.6.2           xfun_0.52                  
 [66] MatrixGenerics_1.18.1       distributional_0.5.0        AUCell_1.28.0               GenomeInfoDb_1.42.3         HDF5Array_1.34.0           
 [71] withr_3.0.2                 BiocManager_1.30.25         fastmap_1.2.0               rhdf5filters_1.18.1         rsvd_1.0.5                 
 [76] digest_0.6.37               R6_2.6.1                    mime_0.13                   colorspace_2.1-1            scattermore_1.2            
 [81] tensor_1.5                  RSQLite_2.4.0               spatstat.data_3.1-6         R.methodsS3_1.8.2           generics_0.1.4             
 [86] data.table_1.17.4           httr_1.4.7                  htmlwidgets_1.6.4           S4Arrays_1.6.0              uwot_0.2.3                 
 [91] pkgconfig_2.0.3             gtable_0.3.6                blob_1.2.4                  lmtest_0.9-40               SingleCellExperiment_1.28.1
 [96] XVector_0.46.0              htmltools_0.5.8.1           carData_3.0-5               dotCall64_1.2               scales_1.4.0               
[101] png_0.1-8                   SpatialExperiment_1.16.0    spatstat.univar_3.1-3       knitr_1.50                  rstudioapi_0.17.1          
[106] rjson_0.2.23                reshape2_1.4.4              nlme_3.1-168                curl_6.2.3                  rhdf5_2.50.2               
[111] cachem_1.1.0                zoo_1.8-14                  KernSmooth_2.23-26          parallel_4.4.2              miniUI_0.1.2               
[116] vipor_0.4.7                 pillar_1.10.2               grid_4.4.2                  vctrs_0.6.5                 RANN_2.6.2                 
[121] promises_1.3.3              BiocSingular_1.22.0         car_3.1-3                   beachmat_2.22.0             xtable_1.8-4               
[126] cluster_2.1.8.1             beeswarm_0.4.0              evaluate_1.0.3              magick_2.8.6                cli_3.6.5                  
[131] compiler_4.4.2              rlang_1.1.6                 crayon_1.5.3                future.apply_1.11.3         ggsignif_0.6.4             
[136] labeling_0.4.3              plyr_1.8.9                  stringi_1.8.7               viridisLite_0.4.2           deldir_2.0-4               
[141] assertthat_0.2.1            babelgene_22.9              Biostrings_2.74.1           lazyeval_0.2.2              spatstat.geom_3.4-1        
[146] RcppHNSW_0.6.0              patchwork_1.3.0             sparseMatrixStats_1.18.0    bit64_4.6.0-1               future_1.49.0              
[151] Rhdf5lib_1.28.0             KEGGREST_1.46.0             statmod_1.5.0               shiny_1.10.0                SummarizedExperiment_1.36.0
[156] ROCR_1.0-11                 memoise_2.0.1               igraph_2.1.4                broom_1.0.8                 bit_4.6.0         

[ncborcherding]

Hey @toobiwankenobi,

Thanks for reaching out - don't think that is the issue. escape supports sparse matrices. I am thinking based on the version of escape, you ran into this problem (#152). A dumb missing final assignment. I am not sure why converting to a full matrix removes the error?

Nick

[toobiwankenobi]

Hi @ncborcherding
As always, thanks for the fast reply. Updating to v2.5.3 did not solve the issue. I guess it is not related to issue #152 then. I'll try to find out where this error is coming from.
Best, Tobi

[ncborcherding]

@toobiwankenobi

Thanks for the follow up - repoening the issue, sorry for the premature closure. If you can make a reproducible example, happy to trooubleshoot with you!!

Nick

[toobiwankenobi]

Hi @ncborcherding

I think I found the issue. Transposing a sparse and compressed matrix of class dgCMatrix only works with Matrix::t() but not with base::t(). That is why this line causes an error in my case.

escape/R/utils.R

Line 197 in a833a6d

sc[[name]] <- fn(data = as.matrix(t(enrichment)))

I would suggest this. I will create a pull request for this.

sc[[name]] <- fn(data = as.matrix(Matrix::t(enrichment)))

Best wishes,
Tobi