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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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Error in loading PBMC dataset for Seurat V5 - Introductory Vignette #9046

Closed LukeStarWars closed 1 week ago

LukeStarWars commented 1 week ago

Hello, after loading what I believe is the correct directory I get an error when trying to load the pbmc dataset for the introductory vignette.

library(dplyr) library(Seurat) library(patchwork) library(SeuratData) InstallData('pbmc3k') pbmc <- LoadData('pbmc3k')

pbmc.data <- Read10X(data.dir = "/brahms/mollag/practice/filtered_gene_bc_matrices/hg19/")

R version 4.4.1 (2024-06-14) Platform: aarch64-apple-darwin20 Running under: macOS Sonoma 14.5

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-arm64/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/Los_Angeles 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 patchwork_1.2.0
[4] Seurat_5.1.0 SeuratObject_5.0.2 sp_2.1-4
[7] dplyr_1.1.4

loaded via a namespace (and not attached): [1] deldir_2.0-4 pbapply_1.7-2 gridExtra_2.3
[4] remotes_2.5.0 rlang_1.1.4 magrittr_2.0.3
[7] RcppAnnoy_0.0.22 spatstat.geom_3.2-9 matrixStats_1.3.0
[10] ggridges_0.5.6 compiler_4.4.1 png_0.1-8
[13] vctrs_0.6.5 reshape2_1.4.4 stringr_1.5.1
[16] profvis_0.3.8 crayon_1.5.3 pkgconfig_2.0.3
[19] fastmap_1.2.0 ellipsis_0.3.2 utf8_1.2.4
[22] promises_1.3.0 sessioninfo_1.2.2 purrr_1.0.2
[25] cachem_1.1.0 jsonlite_1.8.8 goftest_1.2-3
[28] later_1.3.2 spatstat.utils_3.0-5 irlba_2.3.5.1
[31] parallel_4.4.1 cluster_2.1.6 R6_2.5.1
[34] ica_1.0-3 spatstat.data_3.1-2 stringi_1.8.4
[37] RColorBrewer_1.1-3 reticulate_1.38.0 parallelly_1.37.1
[40] pkgload_1.3.4 lmtest_0.9-40 scattermore_1.2
[43] Rcpp_1.0.12 tensor_1.5 future.apply_1.11.2
[46] usethis_2.2.3 zoo_1.8-12 sctransform_0.4.1
[49] httpuv_1.6.15 Matrix_1.7-0 splines_4.4.1
[52] igraph_2.0.3 tidyselect_1.2.1 abind_1.4-5
[55] rstudioapi_0.16.0 spatstat.random_3.2-3 spatstat.explore_3.2-7 [58] codetools_0.2-20 miniUI_0.1.1.1 listenv_0.9.1
[61] pkgbuild_1.4.4 lattice_0.22-6 tibble_3.2.1
[64] plyr_1.8.9 shiny_1.8.1.1 ROCR_1.0-11
[67] Rtsne_0.17 future_1.33.2 fastDummies_1.7.3
[70] survival_3.7-0 polyclip_1.10-6 urlchecker_1.0.1
[73] fitdistrplus_1.1-11 pillar_1.9.0 KernSmooth_2.23-24
[76] plotly_4.10.4 generics_0.1.3 RcppHNSW_0.6.0
[79] ggplot2_3.5.1 munsell_0.5.1 scales_1.3.0
[82] globals_0.16.3 xtable_1.8-4 glue_1.7.0
[85] lazyeval_0.2.2 tools_4.4.1 data.table_1.15.4
[88] RSpectra_0.16-1 RANN_2.6.1 fs_1.6.4
[91] leiden_0.4.3.1 dotCall64_1.1-1 cowplot_1.1.3
[94] grid_4.4.1 tidyr_1.3.1 devtools_2.4.5
[97] colorspace_2.1-0 nlme_3.1-165 cli_3.6.3
[100] rappdirs_0.3.3 spatstat.sparse_3.1-0 spam_2.10-0
[103] fansi_1.0.6 viridisLite_0.4.2 uwot_0.2.2
[106] gtable_0.3.5 digest_0.6.36 progressr_0.14.0
[109] ggrepel_0.9.5 htmlwidgets_1.6.4 memoise_2.0.1
[112] htmltools_0.5.8.1 lifecycle_1.0.4 httr_1.4.7
[115] mime_0.12 MASS_7.3-61

insert reproducible example here


> pbmc.data <- Read10X(data.dir = "/brahms/mollag/practice/filtered_gene_bc_matrices/hg19/")
Error in Read10X(data.dir = "/brahms/mollag/practice/filtered_gene_bc_matrices/hg19/") : 
  Directory provided does not exist
Gesmira commented 1 week ago

Hi, That path exists on my personal computer :) You will have to download the raw data which can be found here and set your own path.