GetAssayData() deprecation warning

[dhcorn]

Hello,

I am trying to use runEscape() and i keep getting the following warning (with the traceback if that is helpful).

Error:
! The slot argument of GetAssayData() was deprecated in SeuratObject 5.0.0 and is now defunct.
ℹ Please use the layer argument instead.

Backtrace:
▆

1. └─escape::runEscape(...)
2. └─escape::escape.matrix(...)

3. └─escape:::.cntEval(input.data, assay = "RNA", type = "counts")
   

4.   ├─base::suppressWarnings(...)
   

5.   │ └─base::withCallingHandlers(...)
   

6.   ├─SeuratObject::GetAssayData(obj, assay = assay, slot = type)
   

7.   └─SeuratObject:::GetAssayData.Seurat(obj, assay = assay, slot = type)
   

8.     └─SeuratObject::.Deprecate(...)
   

9.       └─lifecycle::deprecate_stop(...)
   

10.         └─lifecycle:::deprecate_stop0(msg)
    

Can I use this package on seurat 5.3.0? Maybe there is something i am not getting right. the following is the code i am trying to use and my current workspace. coinf.obj is my gene expression only seurat object but i have also tried this with my VDJ and GEX combined object. The objects also has 3 samples merged together and run through the basic seurat pipline.

gene_sets <- getGeneSets(species = "Mus musculus")

coinf.obj <- runEscape(coinf.obj,
method = "GSVA",
gene.sets = gene_sets,
groups = 1000,
min.size = 3,
new.assay.name = "GSVA")

sessionInfo()
R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.1.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1

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/Denver
tzcode source: internal

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

other attached packages:
[1] EnhancedVolcano_1.28.2 ggrepel_0.9.6 pheatmap_1.0.13 apeglm_1.32.0 DESeq2_1.50.2 SummarizedExperiment_1.40.0 Biobase_2.70.0
[8] MatrixGenerics_1.22.0 matrixStats_1.5.0 GenomicRanges_1.62.1 Seqinfo_1.0.0 IRanges_2.44.0 S4Vectors_0.48.0 BiocGenerics_0.56.0
[15] generics_0.1.4 enrichR_3.4 scplotter_0.4.0 escape_2.6.1 ggraph_2.2.2 RColorBrewer_1.1-3 viridis_0.6.5
[22] viridisLite_0.4.2 future_1.68.0 dplyr_1.1.4 ComplexHeatmap_2.26.0 devtools_2.4.6 usethis_3.2.1 tictoc_1.2.1
[29] scales_1.4.0 circlize_0.4.17 stringr_1.6.0 cowplot_1.2.0 ggalluvial_0.12.5 scRepertoire_2.6.2 ggplot2_4.0.1
[36] presto_1.0.0 data.table_1.17.8 Rcpp_1.1.0 Seurat_5.4.0 SeuratObject_5.3.0 sp_2.2-0

loaded via a namespace (and not attached):
[1] fs_1.6.6 spatstat.sparse_3.1-0 httr_1.4.7 doParallel_1.0.17 numDeriv_2016.8-1.1 tools_4.5.1 sctransform_0.4.2
[8] R6_2.6.1 lazyeval_0.2.2 uwot_0.2.4 ggdist_3.3.3 GetoptLong_1.1.0 withr_3.0.2 gridExtra_2.3
[15] progressr_0.18.0 quantreg_6.1 cli_3.6.5 spatstat.explore_3.6-0 fastDummies_1.7.5 iNEXT_3.0.2 isoband_0.3.0
[22] labeling_0.4.3 mvtnorm_1.3-3 S7_0.2.1 spatstat.data_3.1-9 ggridges_0.5.7 pbapply_1.7-4 R.utils_2.13.0
[29] parallelly_1.46.0 WriteXLS_6.8.0 sessioninfo_1.2.3 bbmle_1.0.25.1 RSQLite_2.4.5 rstudioapi_0.17.1 shape_1.4.6.1
[36] ica_1.0-3 spatstat.random_3.4-3 distributional_0.5.0 Matrix_1.7-4 abind_1.4-8 R.methodsS3_1.8.2 lifecycle_1.0.4
[43] yaml_2.3.12 SparseArray_1.10.6 Rtsne_0.17 blob_1.2.4 promises_1.5.0 crayon_1.5.3 bdsmatrix_1.3-7
[50] miniUI_0.1.2 lattice_0.22-7 annotate_1.88.0 KEGGREST_1.50.0 pillar_1.11.1 knitr_1.50 rjson_0.2.23
[57] future.apply_1.20.1 codetools_0.2-20 glue_1.8.0 spatstat.univar_3.1-5 remotes_2.5.0 vctrs_0.6.5 png_0.1-8
[64] spam_2.11-1 gtable_0.3.6 emdbook_1.3.14 cachem_1.1.0 xfun_0.55 S4Arrays_1.10.1 mime_0.13
[71] tidygraph_1.3.1 coda_0.19-4.1 survival_3.8-3 SingleCellExperiment_1.32.0 iterators_1.0.14 ellipsis_0.3.2 fitdistrplus_1.2-4
[78] ROCR_1.0-11 nlme_3.1-168 bit64_4.6.0-1 RcppAnnoy_0.0.22 irlba_2.3.5.1 KernSmooth_2.23-26 otel_0.2.0
[85] DBI_1.2.3 plotthis_0.9.0 colorspace_2.1-2 tidyselect_1.2.1 bit_4.6.0 compiler_4.5.1 curl_7.0.0
[92] graph_1.88.1 rvest_1.0.5 SparseM_1.84-2 xml2_1.5.1 ggdendro_0.2.0 DelayedArray_0.36.0 plotly_4.11.0
[99] lmtest_0.9-40 digest_0.6.39 goftest_1.2-3 spatstat.utils_3.2-0 rmarkdown_2.30 XVector_0.50.0 htmltools_0.5.9
[106] pkgconfig_2.0.3 fastmap_1.2.0 rlang_1.1.6 GlobalOptions_0.1.3 htmlwidgets_1.6.4 shiny_1.12.1 immApex_1.4.3
[113] farver_2.1.2 zoo_1.8-15 jsonlite_2.0.0 BiocParallel_1.44.0 R.oo_1.27.1 magrittr_2.0.4 dotCall64_1.2
[120] patchwork_1.3.2 evmix_2.12 ggnewscale_0.5.2 reticulate_1.44.1 stringi_1.8.7 MASS_7.3-65 plyr_1.8.9
[127] pkgbuild_1.4.8 parallel_4.5.1 listenv_0.10.0 forcats_1.0.1 deldir_2.0-4 Biostrings_2.78.0 graphlayouts_1.2.2
[134] splines_4.5.1 gridtext_0.1.5 tensor_1.5.1 hash_2.2.6.3 locfit_1.5-9.12 igraph_2.2.1 spatstat.geom_3.6-1
[141] RcppHNSW_0.6.0 reshape2_1.4.5 pkgload_1.4.1 XML_3.99-0.20 evaluate_1.0.5 foreach_1.5.2 tweenr_2.0.3
[148] httpuv_1.6.16 MatrixModels_0.5-4 RANN_2.6.2 tidyr_1.3.1 purrr_1.2.0 polyclip_1.10-7 clue_0.3-66
[155] scattermore_1.2 ggforce_0.5.0 xtable_1.8-4 RSpectra_0.16-2 later_1.4.4 gsl_2.1-9 tibble_3.3.0
[162] AnnotationDbi_1.72.0 memoise_2.0.1 cluster_2.1.8.1 globals_0.18.0 GSEABase_1.72.0

THank you in advance for your help with this.

[ncborcherding]

Hey @dhcorn

Appreciate the issue and rundown - this is due to the official deprecation of the slot argument in the newest versions of Seurat. I have fixed this (#176) and you should be able to get things working with a fresh install of escape:

devtools::install_github("BorchLab/escape")

Make sure you restart your R session aftering updating and you should be good to go. I have already pushed the changes to Bioconductor, but sometimes there is a delay in the builds.

Hope that helps,

Nick