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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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SeuratData sets are not working #7772

Closed marlmatos closed 1 year ago

marlmatos commented 1 year ago

Hi, I installed SeuratData pmbc3k and pbcmcsa to try to follow this vignette https://satijalab.org/seurat/articles/integration_mapping.html because azimuth was not working for me, and I am able to load the datasets into my R session but none of the seurat functions work on them. I keep getting this error.

Error in slot(object = object, name = s) : no slot of name "images" for this object of class "Seurat"

Yes, I reran this bug in two different sessions in two different machines

# insert reproducible example here
library(Seurat)
devtools::install_github('satijalab/seurat-data')
library(SeuratData)
InstallData("pbmc3k")
> pbmc3k <- LoadData("pbmc3k" )
> pbmc3k <- NormalizeData(pbmc3k, verbose = FALSE)
Error in slot(object = object, name = s) : 
  no slot of name "images" for this object of class "Seurat"
> pbmc3k <- FindVariableFeatures(pbmc3k, selection.method = "vst", nfeatures = 2000,
+                                verbose = FALSE)
Error in slot(object = object, name = s) : 
  no slot of name "images" for this object of class "Seurat"

sessionInfo() ` R version 4.3.0 (2023-04-21) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.4

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

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] stats graphics grDevices utils datasets methods base

other attached packages: [1] pbmc3k.SeuratData_3.1.4 SeuratData_0.2.2 Seurat_4.9.9.9050 SeuratObject_4.9.9.9086 sp_2.0-0
[6] ViSEAGO_1.14.0

loaded via a namespace (and not attached): [1] fs_1.6.3 spatstat.sparse_3.0-2 matrixStats_1.0.0 bitops_1.0-7 enrichplot_1.20.1
[6] devtools_2.4.5 HDO.db_0.99.1 httr_1.4.7 webshot_0.5.5 RColorBrewer_1.1-3
[11] dynamicTreeCut_1.63-1 profvis_0.3.8 tools_4.3.0 sctransform_0.3.5 utf8_1.2.3
[16] R6_2.5.1 DT_0.29 uwot_0.1.16 lazyeval_0.2.2 urlchecker_1.0.1
[21] withr_2.5.0 prettyunits_1.1.1 gridExtra_2.3 progressr_0.14.0 cli_3.6.1
[26] Biobase_2.60.0 spatstat.explore_3.2-1 fastDummies_1.7.3 TSP_1.2-4 scatterpie_0.2.1
[31] topGO_2.52.0 spatstat.data_3.0-1 ggridges_0.5.4 pbapply_1.7-2 yulab.utils_0.0.9
[36] gson_0.1.0 DOSE_3.26.1 R.utils_2.12.2 AnnotationForge_1.42.2 sessioninfo_1.2.2
[41] parallelly_1.36.0 rstudioapi_0.15.0 RSQLite_2.3.1 visNetwork_2.1.2 generics_0.1.3
[46] gridGraphics_0.5-1 spatstat.random_3.1-5 ica_1.0-3 dplyr_1.1.2 dendextend_1.17.1
[51] GO.db_3.17.0 Matrix_1.6-1 fansi_1.0.4 S4Vectors_0.38.1 abind_1.4-5
[56] R.methodsS3_1.8.2 lifecycle_1.0.3 yaml_2.3.7 qvalue_2.32.0 BiocFileCache_2.8.0
[61] Rtsne_0.16 grid_4.3.0 blob_1.2.4 promises_1.2.1 crayon_1.5.2
[66] miniUI_0.1.1.1 lattice_0.21-8 cowplot_1.1.1 KEGGREST_1.40.0 pillar_1.9.0
[71] knitr_1.43 fgsea_1.26.0 future.apply_1.11.0 codetools_0.2-19 fastmatch_1.1-4
[76] leiden_0.4.3 glue_1.6.2 downloader_0.4 ggfun_0.1.2 remotes_2.4.2.1
[81] data.table_1.14.8 vctrs_0.6.3 png_0.1-8 treeio_1.24.3 spam_2.9-1
[86] gtable_0.3.4 assertthat_0.2.1 cachem_1.0.8 xfun_0.40 mime_0.12
[91] tidygraph_1.2.3 survival_3.5-7 seriation_1.5.1 iterators_1.0.14 DiagrammeR_1.0.10
[96] ellipsis_0.3.2 fitdistrplus_1.1-11 ROCR_1.0-11 nlme_3.1-163 usethis_2.2.2
[101] ggtree_3.8.2 bit64_4.0.5 progress_1.2.2 filelock_1.0.2 RcppAnnoy_0.0.21
[106] rprojroot_2.0.3 UpSetR_1.4.0 GenomeInfoDb_1.36.2 irlba_2.3.5.1 KernSmooth_2.23-22
[111] colorspace_2.1-0 BiocGenerics_0.46.0 DBI_1.1.3 processx_3.8.2 tidyselect_1.2.0
[116] bit_4.0.5 compiler_4.3.0 curl_5.0.2 graph_1.78.0 SparseM_1.81
[121] xml2_1.3.5 desc_1.4.2 plotly_4.10.2 shadowtext_0.1.2 scales_1.2.1
[126] lmtest_0.9-40 callr_3.7.3 rappdirs_0.3.3 goftest_1.2-3 stringr_1.5.0
[131] digest_0.6.33 spatstat.utils_3.0-3 rmarkdown_2.24 ca_0.71.1 XVector_0.40.0
[136] htmltools_0.5.6 pkgconfig_2.0.3 dbplyr_2.3.3 fastmap_1.1.1 rlang_1.1.1
[141] htmlwidgets_1.6.2 shiny_1.7.5 farver_2.1.1 zoo_1.8-12 jsonlite_1.8.7
[146] BiocParallel_1.34.2 GOSemSim_2.26.1 R.oo_1.25.0 RCurl_1.98-1.12 magrittr_2.0.3
[151] GenomeInfoDbData_1.2.10 ggplotify_0.1.2 dotCall64_1.0-2 patchwork_1.1.3 munsell_0.5.0
[156] Rcpp_1.0.11 ape_5.7-1 ggnewscale_0.4.9 viridis_0.6.4 reticulate_1.31
[161] stringi_1.7.12 ggraph_2.1.0 zlibbioc_1.46.0 MASS_7.3-60 pkgbuild_1.4.2
[166] plyr_1.8.8 parallel_4.3.0 listenv_0.9.0 ggrepel_0.9.3 deldir_1.0-9
[171] Biostrings_2.68.1 graphlayouts_1.0.0 splines_4.3.0 tensor_1.5 hms_1.1.3
[176] ps_1.7.5 igraph_1.5.1 spatstat.geom_3.2-4 RcppHNSW_0.4.1 pkgload_1.3.2.1
[181] reshape2_1.4.4 biomaRt_2.56.1 stats4_4.3.0 XML_3.99-0.14 evaluate_0.21
[186] foreach_1.5.2 tweenr_2.0.2 httpuv_1.6.11 RANN_2.6.1 tidyr_1.3.0
[191] purrr_1.0.2 polyclip_1.10-4 future_1.33.0 heatmaply_1.4.2 scattermore_1.2
[196] ggplot2_3.4.3 ggforce_0.4.1 xtable_1.8-4 RSpectra_0.16-1 tidytree_0.4.5
[201] later_1.3.1 viridisLite_0.4.2 tibble_3.2.1 clusterProfiler_4.8.3 aplot_0.2.0
[206] memoise_2.0.1 AnnotationDbi_1.62.2 registry_0.5-1 IRanges_2.34.1 cluster_2.1.4
[211] globals_0.16.2 `

Gesmira commented 1 year ago

Hi, Since you're using Seurat v5 you have to run: pbmc3k <- UpdateSeuratObject(pbmc3k) after you load it in if you're not defaulting to options(Seurat.object.assay.version = "v5"). After that, the rest of the functions should work normally.