Issue with IntegrateData

[qiuwwenlf]

When I run the function IntegrateData() in Seurat 5.03, I got the following error:
Error in .rowNamesDF<-(x, value = value) : invalid 'row.names' length
And the code is:
scRNAepithelial.anchors <- FindIntegrationAnchors(object.list = scRNAepithelial.list,
anchor.features = features)
scRNAepithelial.combined <- IntegrateData(anchorset = scRNAepithelial.anchors)
This is the old code, and I had run it with no error before.

[Joy8Liu]

I have the same issue when using "IntegrateData" and "merge" function, both using data after SCT in Seurat 5.1.0

By the way, "merge" function is good when using raw data.

SessionInfo

R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /public/software/apps/R-4.3.1/lib64/R/lib/libRblas.so 
LAPACK: /public/software/apps/R-4.3.1/lib64/R/lib/libRlapack.so;  LAPACK version 3.11.0

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

other attached packages:
 [1] job_0.3.1           future.apply_1.11.2 future_1.33.2      
 [4] rmarkdown_2.26      cowplot_1.1.3       sctransform_0.4.1  
 [7] DoubletFinder_2.0.4 glmGamPoi_1.14.3    ggplot2_3.5.1      
[10] patchwork_1.2.0     dplyr_1.1.4         Seurat_5.1.0       
[13] SeuratObject_5.0.2  sp_2.1-4           

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3          rstudioapi_0.16.0          
  [3] jsonlite_1.8.8              magrittr_2.0.3             
  [5] spatstat.utils_3.0-4        zlibbioc_1.48.2            
  [7] vctrs_0.6.5                 ROCR_1.0-11                
  [9] spatstat.explore_3.2-7      RCurl_1.98-1.14            
 [11] S4Arrays_1.2.1              htmltools_0.5.8.1          
 [13] SparseArray_1.2.4           parallelly_1.37.1          
 [15] KernSmooth_2.23-22          htmlwidgets_1.6.4          
 [17] ica_1.0-3                   plyr_1.8.9                 
 [19] plotly_4.10.4               zoo_1.8-12                 
 [21] igraph_2.0.3                mime_0.12                  
 [23] lifecycle_1.0.4             pkgconfig_2.0.3            
 [25] Matrix_1.6-4                R6_2.5.1                   
 [27] fastmap_1.1.1               GenomeInfoDbData_1.2.11    
 [29] MatrixGenerics_1.14.0       fitdistrplus_1.1-11        
 [31] shiny_1.8.1.1               digest_0.6.35              
 [33] colorspace_2.1-0            S4Vectors_0.40.2           
 [35] tensor_1.5                  RSpectra_0.16-1            
 [37] irlba_2.3.5.1               GenomicRanges_1.54.1       
 [39] progressr_0.14.0            fansi_1.0.6                
 [41] spatstat.sparse_3.0-3       httr_1.4.7                 
 [43] polyclip_1.10-6             abind_1.4-5                
 [45] compiler_4.3.1              withr_3.0.0                
 [47] fastDummies_1.7.3           MASS_7.3-60                
 [49] DelayedArray_0.28.0         tools_4.3.1                
 [51] lmtest_0.9-40               httpuv_1.6.15              
 [53] goftest_1.2-3               glue_1.7.0                 
 [55] nlme_3.1-164                promises_1.3.0             
 [57] grid_4.3.1                  Rtsne_0.17                 
 [59] cluster_2.1.6               reshape2_1.4.4             
 [61] generics_0.1.3              gtable_0.3.5               
 [63] spatstat.data_3.0-4         tidyr_1.3.1                
 [65] data.table_1.15.4           utf8_1.2.4                 
 [67] XVector_0.42.0              BiocGenerics_0.48.1        
 [69] spatstat.geom_3.2-9         RcppAnnoy_0.0.22           
 [71] ggrepel_0.9.5               RANN_2.6.1                 
 [73] pillar_1.9.0                stringr_1.5.1              
 [75] spam_2.10-0                 RcppHNSW_0.6.0             
 [77] later_1.3.2                 splines_4.3.1              
 [79] lattice_0.22-6              survival_3.6-4             
 [81] deldir_2.0-4                tidyselect_1.2.1           
 [83] miniUI_0.1.1.1              pbapply_1.7-2              
 [85] knitr_1.46                  gridExtra_2.3              
 [87] IRanges_2.36.0              SummarizedExperiment_1.32.0
 [89] scattermore_1.2             stats4_4.3.1               
 [91] xfun_0.43                   Biobase_2.62.0             
 [93] matrixStats_1.3.0           stringi_1.8.4              
 [95] yaml_2.3.8                  pacman_0.5.1               
 [97] lazyeval_0.2.2              evaluate_0.23              
 [99] codetools_0.2-20            tibble_3.2.1               
[101] BiocManager_1.30.22         cli_3.6.2                  
[103] uwot_0.2.2                  xtable_1.8-4               
[105] reticulate_1.36.1           munsell_0.5.1              
[107] Rcpp_1.0.12                 GenomeInfoDb_1.38.8        
[109] globals_0.16.3              spatstat.random_3.2-3      
[111] png_0.1-8                   parallel_4.3.1             
[113] dotCall64_1.1-1             bitops_1.0-7               
[115] listenv_0.9.1               viridisLite_0.4.2          
[117] scales_1.3.0                ggridges_0.5.6             
[119] crayon_1.5.2                leiden_0.4.3.1             
[121] purrr_1.0.2                 rlang_1.1.3