Integration single-cell data with spatial transcriptomic from 10x Visium

[TiphaineCMartin]

Hi,

I try to integrate single-cell data with spatial transcriptomics from 10x Visium.

As described in issue 9702, I have a memory issue when transforming my single-cell data.

I transform spatial transcriptomic

HFD8 <- SCTransform(HFD8, assay = "Spatial", verbose = FALSE)

I wanted to join with the single-cell data that I have, but I met the error about different normalization.

anchors <- FindTransferAnchors(reference = adipose.raw, query = HFD8)
Error: An SCT assay (SCT) was provided for query.assay but normalization.method was set as LogNormalize

anchors <- FindTransferAnchors(reference = adipose.raw, query = HFD8,
+                                normalization.method = "SCT")
Error in slot(object = reference[[reference.assay]], name = "SCTModel.list") : 
  no slot of name "SCTModel.list" for this object of class "Assay5"

what do you propose the best to manage the memory issue and normalization between two objects?

thanks,
Tiphaine

sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-apple-darwin20
Running under: macOS Sequoia 15.3.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/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: America/New_York
tzcode source: internal

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

other attached packages:
 [1] glmGamPoi_1.16.0            reshape2_1.4.4              future_1.34.0              
 [4] shiny_1.10.0                monocle3_1.3.7              SingleCellExperiment_1.26.0
 [7] SummarizedExperiment_1.34.0 GenomicRanges_1.56.2        GenomeInfoDb_1.40.1        
[10] IRanges_2.38.1              S4Vectors_0.42.1            MatrixGenerics_1.16.0      
[13] matrixStats_1.5.0           Biobase_2.64.0              BiocGenerics_0.50.0        
[16] lubridate_1.9.4             forcats_1.0.0               purrr_1.0.4                
[19] readr_2.1.5                 tidyr_1.3.1                 tibble_3.2.1               
[22] tidyverse_2.0.0             RColorBrewer_1.1-3          stringr_1.5.1              
[25] ggthemes_5.1.0              ggbeeswarm_0.7.2            plotly_4.10.4              
[28] destiny_3.18.0              SeuratWrappers_0.3.2        wesanderson_0.3.7          
[31] ggsci_3.2.0                 patchwork_1.3.0             harmony_1.2.3              
[34] Rcpp_1.0.14                 Matrix_1.7-2                Seurat_5.2.1               
[37] SeuratObject_5.0.2          sp_2.2-0                    ggplot2_3.5.1              
[40] ggridges_0.5.6              viridis_0.6.5               viridisLite_0.4.2          
[43] data.table_1.16.4           dplyr_1.1.4                

loaded via a namespace (and not attached):
  [1] spatstat.sparse_3.1-0     httr_1.4.7                tools_4.4.2              
  [4] sctransform_0.4.1         R6_2.6.1                  lazyeval_0.2.2           
  [7] uwot_0.2.2                withr_3.0.2               gridExtra_2.3            
 [10] progressr_0.15.1          textshaping_1.0.0         cli_3.6.4                
 [13] spatstat.explore_3.3-4    fastDummies_1.7.5         isoband_0.2.7            
 [16] sass_0.4.9                labeling_0.4.3            robustbase_0.99-4-1      
 [19] spatstat.data_3.1-4       proxy_0.4-27              pbapply_1.7-2            
 [22] systemfonts_1.2.1         R.utils_2.12.3            parallelly_1.42.0        
 [25] Rfast2_0.1.5.2            limma_3.60.6              TTR_0.24.4               
 [28] rstudioapi_0.17.1         generics_0.1.3            crosstalk_1.2.1          
 [31] ica_1.0-3                 spatstat.random_3.3-2     car_3.1-3                
 [34] abind_1.4-8               R.methodsS3_1.8.2         lifecycle_1.0.4          
 [37] yaml_2.3.10               scatterplot3d_0.3-44      carData_3.0-5            
 [40] SparseArray_1.4.8         Rtsne_0.17                promises_1.3.2           
 [43] crayon_1.5.3              miniUI_0.1.1.1            lattice_0.22-6           
 [46] cowplot_1.1.3             knitr_1.49                pillar_1.10.1            
 [49] boot_1.3-31               future.apply_1.11.3       codetools_0.2-20         
 [52] Rnanoflann_0.0.3          glue_1.8.0                leidenbase_0.1.32        
 [55] spatstat.univar_3.1-1     pcaMethods_1.96.0         remotes_2.5.0            
 [58] vcd_1.4-13                Rdpack_2.6.2              vctrs_0.6.5              
 [61] png_0.1-8                 spam_2.11-1               gtable_0.3.6             
 [64] assertthat_0.2.1          cachem_1.1.0              xfun_0.50                
 [67] rbibutils_2.3             S4Arrays_1.4.1            mime_0.12                
 [70] Rfast_2.1.4               RcppEigen_0.3.4.0.2       reformulas_0.4.0         
 [73] survival_3.8-3            statmod_1.5.0             fitdistrplus_1.2-2       
 [76] ROCR_1.0-11               nlme_3.1-167              xts_0.14.1               
 [79] bit64_4.6.0-1             RcppAnnoy_0.0.22          bslib_0.9.0              
 [82] irlba_2.3.5.1             vipor_0.4.7               KernSmooth_2.23-26       
 [85] colorspace_2.1-1          nnet_7.3-20               ggrastr_1.0.2            
 [88] tidyselect_1.2.1          smoother_1.3              processx_3.8.5           
 [91] bit_4.5.0.1               compiler_4.4.2            curl_6.2.0               
 [94] hdf5r_1.3.12              desc_1.4.3                DelayedArray_0.30.1      
 [97] scales_1.3.0              DEoptimR_1.1-3-1          lmtest_0.9-40            
[100] hexbin_1.28.5             callr_3.7.6               digest_0.6.37            
[103] goftest_1.2-3             presto_1.0.0              spatstat.utils_3.1-2     
[106] minqa_1.2.8               rmarkdown_2.29            XVector_0.44.0           
[109] htmltools_0.5.8.1         pkgconfig_2.0.3           lme4_1.1-36              
[112] sparseMatrixStats_1.16.0  fastmap_1.2.0             rlang_1.1.5              
[115] htmlwidgets_1.6.4         UCSC.utils_1.0.0          DelayedMatrixStats_1.26.0
[118] jquerylib_0.1.4           farver_2.1.2              zoo_1.8-12               
[121] jsonlite_1.8.9            R.oo_1.27.0               magrittr_2.0.3           
[124] Formula_1.2-5             GenomeInfoDbData_1.2.12   dotCall64_1.2            
[127] munsell_0.5.1             reticulate_1.40.0         RcppZiggurat_0.1.6       
[130] stringi_1.8.4             zlibbioc_1.50.0           MASS_7.3-64              
[133] plyr_1.8.9                pkgbuild_1.4.6            parallel_4.4.2           
[136] listenv_0.9.1             ggrepel_0.9.6             deldir_2.0-4             
[139] splines_4.4.2             tensor_1.5                hms_1.1.3                
[142] ps_1.8.1                  igraph_2.1.4              ranger_0.17.0            
[145] spatstat.geom_3.3-5       RcppHNSW_0.6.0            evaluate_1.0.3           
[148] RcppParallel_5.1.10       BiocManager_1.30.25       laeken_0.5.3             
[151] nloptr_2.1.1              tzdb_0.4.0                httpuv_1.6.15            
[154] VIM_6.2.2                 RANN_2.6.2                polyclip_1.10-7          
[157] knn.covertree_1.0         scattermore_1.2           rsvd_1.0.5               
[160] xtable_1.8-4              e1071_1.7-16              RSpectra_0.16-2          
[163] later_1.4.1               ragg_1.3.3                class_7.3-23             
[166] memoise_2.0.1             beeswarm_0.4.0            cluster_2.1.8            
[169] ggplot.multistats_1.0.1   timechange_0.3.0          globals_0.16.3