Incompatible matrix dimensions: 100x2 and 2x1 for tutorial data

[pakiessling]

Hi,

I am trying to follow the tutorial:

library(iSpatial)
library(Seurat)
library(ggplot2)

# scRNA-seq data
data(NA_scRNA)

# merFISH data
data(NA_merFISH)
NA_merFISH_infer = infer_v2(NA_merFISH, NA_scRNA)

but I receive the following error:

1st level integration

Warning message:
“Adding image data that isn't associated with any assays”
Warning message:
“Adding image data that isn't associated with any assays”
Warning message:
“Adding image data that isn't associated with any assays”
2nd level integration

Error in eval(expr, envir, enclos): element-wise pow(): incompatible matrix dimensions: 100x2 and 2x1
Traceback:

1. infer_v2(NA_merFISH, NA_scRNA)
2. suppressWarnings(harmony::RunHarmony(object = integrated, group.by.vars = "tech", 
 .     plot_convergence = F, theta = 2, lambda = 0.5, assay.use = "integrated", 
 .     verbose = FALSE, max.iter.harmony = 20))
3. withCallingHandlers(expr, warning = function(w) if (inherits(w, 
 .     classes)) tryInvokeRestart("muffleWarning"))
4. harmony::RunHarmony(object = integrated, group.by.vars = "tech", 
 .     plot_convergence = F, theta = 2, lambda = 0.5, assay.use = "integrated", 
 .     verbose = FALSE, max.iter.harmony = 20)
5. RunHarmony.Seurat(object = integrated, group.by.vars = "tech", 
 .     plot_convergence = F, theta = 2, lambda = 0.5, assay.use = "integrated", 
 .     verbose = FALSE, max.iter.harmony = 20)
6. HarmonyMatrix(embedding, metavars_df, group.by.vars, FALSE, 0, 
 .     theta, lambda, sigma, nclust, tau, block.size, max.iter.harmony, 
 .     max.iter.cluster, epsilon.cluster, epsilon.harmony, plot_convergence, 
 .     FALSE, verbose, reference_values)
7. harmonize(harmonyObj, max.iter.harmony, verbose)
8. cluster(harmonyObj)
9. harmonyObj$cluster_cpp()

Any idea what is going wrong?

[Czh3]

I believe this is caused by the new version V5 of Seurat you used. Can you provide the session infor by running sessionInfo() in R.

[pakiessling]

Ah yeah, it said something about loading the objects in compatibility mode.

I will trying downgrading Seutat later, thank you!

[pakiessling]

I downgraded Seuratobject from 5.0.0 to 4.1.3, but I still receive the same error. sessionInfo():

R version 4.3.1 (2023-06-16)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Rocky Linux 8.8 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: [/rwthfs/rz/cluster/work/rwth1209/enviroments/iSpatial/lib/libopenblasp-r0.3.24.so](https://vscode-remote+ssh-002dremote-002blogin18-002d2-002ehpc-002eitc-002erwth-002daachen-002ede.vscode-resource.vscode-cdn.net/rwthfs/rz/cluster/work/rwth1209/enviroments/iSpatial/lib/libopenblasp-r0.3.24.so);  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: :/etc/localtime
tzcode source: system (glibc)

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

other attached packages:
[1] ggplot2_3.4.4      SeuratObject_4.1.4 Seurat_4.4.0       iSpatial_1.0.0    

loaded via a namespace (and not attached):
  [1] deldir_1.0-9           pbapply_1.7-2          gridExtra_2.3         
  [4] rlang_1.1.1            magrittr_2.0.3         RcppAnnoy_0.0.21      
  [7] spatstat.geom_3.2-7    matrixStats_1.0.0      ggridges_0.5.4        
 [10] compiler_4.3.1         png_0.1-8              vctrs_0.6.4           
 [13] reshape2_1.4.4         stringr_1.5.0          pkgconfig_2.0.3       
 [16] crayon_1.5.2           fastmap_1.1.1          ellipsis_0.3.2        
 [19] utf8_1.2.4             promises_1.2.1         purrr_1.0.2           
 [22] jsonlite_1.8.7         goftest_1.2-3          later_1.3.1           
 [25] uuid_1.1-1             spatstat.utils_3.0-4   irlba_2.3.5.1         
 [28] parallel_4.3.1         cluster_2.1.4          R6_2.5.1              
 [31] ica_1.0-3              spatstat.data_3.0-3    stringi_1.7.12        
 [34] RColorBrewer_1.1-3     reticulate_1.34.0      parallelly_1.36.0     
 [37] lmtest_0.9-40          scattermore_1.2        Rcpp_1.0.11           
 [40] IRkernel_1.3.2         tensor_1.5             future.apply_1.11.0   
 [43] zoo_1.8-12             base64enc_0.1-3        sctransform_0.4.1     
 [46] httpuv_1.6.12          Matrix_1.6-1.1         splines_4.3.1         
 [49] igraph_1.5.1           tidyselect_1.2.0       abind_1.4-5           
 [52] spatstat.random_3.2-1  codetools_0.2-19       miniUI_0.1.1.1        
 [55] spatstat.explore_3.2-5 listenv_0.9.0          lattice_0.22-5        
 [58] tibble_3.2.1           plyr_1.8.9             withr_2.5.2           
 [61] shiny_1.7.5.1          ROCR_1.0-11            evaluate_0.22         
 [64] Rtsne_0.16             future_1.33.0          survival_3.5-7        
 [67] polyclip_1.10-6        fitdistrplus_1.1-11    pillar_1.9.0          
 [70] KernSmooth_2.23-22     plotly_4.10.3          generics_0.1.3        
 [73] sp_2.1-1               IRdisplay_1.1          munsell_0.5.0         
 [76] scales_1.2.1           globals_0.16.2         xtable_1.8-4          
 [79] glue_1.6.2             lazyeval_0.2.2         tools_4.3.1           
 [82] data.table_1.14.8      pbdZMQ_0.3-10          RANN_2.6.1            
 [85] leiden_0.4.3           dotCall64_1.1-0        cowplot_1.1.1         
 [88] grid_4.3.1             tidyr_1.3.0            colorspace_2.1-0      
 [91] nlme_3.1-163           patchwork_1.1.3        repr_1.1.6            
 [94] cli_3.6.1              spatstat.sparse_3.0-3  spam_2.9-1            
 [97] fansi_1.0.5            viridisLite_0.4.2      dplyr_1.1.3           
[100] uwot_0.1.16            gtable_0.3.4           digest_0.6.33         
[103] progressr_0.14.0       ggrepel_0.9.4          htmlwidgets_1.6.2     
[106] htmltools_0.5.6.1      lifecycle_1.0.3        httr_1.4.7            
[109] mime_0.12              harmony_1.0            MASS_7.3-60

[Czh3]

Can you check the Version of NA_merFISH Object: Version(NA_merFISH) . You may reinstall or reload iSpatial.

[pakiessling]

Version(NA_merFISH)
> [1] ‘3.1.5.9900’

[pakiessling]

Resolved by updating Harmony to the latest version