Error in SCTransform: Missing cell.attr Argument When Regressing mitoRatio

[EsToHi]

Hi,

When applying SCTransform to individual elements within my data and same for the pbmc3k example data, I encounter an error that indicates a missing argument (cell.attr). This issue arises even when specifying the vars.to.regress parameter. I expected SCTransform to process each object without error, adjusting for mitoRatio in each case.
That's the error:
`for (i in 1:length(pbmc3k)) {

• pbmc3k[[i]] <- SCTransform(pbmc3k[[i]], verbose = FALSE,vars.to.regress = c("mitoRatio"), vst.flavor = "v2")
• }
  Error in SCTransform.default(pbmc3k[[i]], verbose = FALSE, vars.to.regress = c("mitoRatio"), :
  argument "cell.attr" is missing, with no default
  In addition: Warning message:
  In matrix(data = as.numeric(x = x), ncol = nc) : NAs introduced by coercion`

That's my session:

sessionInfo()
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] pbmc3k.SeuratData_3.1.4 SeuratData_0.2.2.9001 Seurat_5.1.0 SeuratObject_5.0.2
[5] sp_2.1-4

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.17.1 jsonlite_1.8.8 magrittr_2.0.3
[5] spatstat.utils_3.0-5 farver_2.1.2 fs_1.6.4 vctrs_0.6.5
[9] ROCR_1.0-11 memoise_2.0.1 spatstat.explore_3.3-1 htmltools_0.5.8.1
[13] usethis_3.0.0 curl_6.0.0 sctransform_0.4.1 parallelly_1.38.0
[17] KernSmooth_2.23-24 htmlwidgets_1.6.4 desc_1.4.3 ica_1.0-3
[21] plyr_1.8.9 plotly_4.10.4 zoo_1.8-12 cachem_1.1.0
[25] igraph_2.0.3 mime_0.12 lifecycle_1.0.4 pkgconfig_2.0.3
[29] Matrix_1.6-5 R6_2.5.1 fastmap_1.2.0 fitdistrplus_1.2-1
[33] future_1.34.0 shiny_1.9.1 digest_0.6.36 colorspace_2.1-0
[37] ps_1.8.1 patchwork_1.3.0 tensor_1.5 RSpectra_0.16-2
[41] irlba_2.3.5.1 pkgload_1.4.0 progressr_0.15.0 fansi_1.0.6
[45] spatstat.sparse_3.1-0 httr_1.4.7 polyclip_1.10-6 abind_1.4-8
[49] compiler_4.3.2 remotes_2.5.0 fastDummies_1.7.4 pkgbuild_1.4.5
[53] MASS_7.3-60 rappdirs_0.3.3 sessioninfo_1.2.2 tools_4.3.2
[57] lmtest_0.9-40 httpuv_1.6.15 future.apply_1.11.3 goftest_1.2-3
[61] glue_1.7.0 callr_3.7.6 nlme_3.1-163 promises_1.3.0
[65] grid_4.3.2 Rtsne_0.17 cluster_2.1.4 reshape2_1.4.4
[69] generics_0.1.3 gtable_0.3.6 spatstat.data_3.1-2 tidyr_1.3.1
[73] data.table_1.15.4 utf8_1.2.4 spatstat.geom_3.3-2 RcppAnnoy_0.0.22
[77] ggrepel_0.9.5 RANN_2.6.1 pillar_1.9.0 stringr_1.5.1
[81] spam_2.10-0 RcppHNSW_0.6.0 later_1.3.2 splines_4.3.2
[85] dplyr_1.1.4 lattice_0.21-9 survival_3.5-7 deldir_2.0-4
[89] tidyselect_1.2.1 miniUI_0.1.1.1 pbapply_1.7-2 gridExtra_2.3
[93] scattermore_1.2 devtools_2.4.5 matrixStats_1.3.0 stringi_1.8.4
[97] lazyeval_0.2.2 codetools_0.2-19 tibble_3.2.1 BiocManager_1.30.25
[101] cli_3.6.3 uwot_0.2.2 xtable_1.8-4 reticulate_1.39.0
[105] munsell_0.5.1 processx_3.8.4 Rcpp_1.0.13 globals_0.16.3
[109] spatstat.random_3.3-1 png_0.1-8 spatstat.univar_3.0-0 parallel_4.3.2
[113] ellipsis_0.3.2 ggplot2_3.5.1 dotCall64_1.1-1 profvis_0.3.8
[117] urlchecker_1.0.1 listenv_0.9.1 viridisLite_0.4.2 scales_1.3.0
[121] ggridges_0.5.6 crayon_1.5.3 leiden_0.4.3.1 purrr_1.0.2
[125] rlang_1.1.4 cowplot_1.1.3

That's reproducible example:

# reproducible example 
devtools::install_github('satijalab/seurat-data', force=T)
library(SeuratData)
InstallData("pbmc3k")
data("pbmc3k")
pbmc3k = UpdateSeuratObject (pbmc3k)
pbmc3k
for (i in 1:length(pbmc3k)) {
  pbmc3k[[i]] <- SCTransform(pbmc3k[[i]], verbose = FALSE,vars.to.regress = c("mitoRatio"), vst.flavor = "v2")
}

Thank you for your help in addressing this issue.