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chuiqin / irGSEA

The integration of single cell rank-based gene set enrichment analysis
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No assay information could be found for ScoreJackStraw #32

Open amingjie228 opened 7 months ago

amingjie228 commented 7 months ago

I encountered an issure when I used this r package. No assay information could be found for ScoreJackStraw Setting assay used for FindNeighbors.RNA.pca to RNA No assay information could be found for FindClusters

devtools::install_github('satijalab/seurat-data')

library(SeuratData) -- Installed datasets ----------------------------------------------------------------------------- SeuratData v0.2.2.9001 -- v pbmc3k 3.1.4

------------------------------------------------------------ Key ------------------------------------------------------------ v Dataset loaded successfully

Dataset built with a newer version of Seurat than installed (?) Unknown version of Seurat installed

view all available datasets

View(AvailableData())

download 3k PBMCs from 10X Genomics

InstallData("pbmc3k") Warning: The following packages are already installed and will not be reinstalled: pbmc3k

the details of pbmc3k.final

?pbmc3k.final

library(Seurat) 载入需要的程辑包：SeuratObject 载入需要的程辑包：sp

载入程辑包：‘SeuratObject’

The following object is masked from ‘package:base’:

intersect

library(SeuratData)

loading dataset

data("pbmc3k.final") pbmc3k.final <- UpdateSeuratObject(pbmc3k.final) Validating object structure Updating object slots Ensuring keys are in the proper structure Updating matrix keys for DimReduc ‘pca’ Updating matrix keys for DimReduc ‘umap’ Warning: Assay RNA changing from Assay to Assay Warning: Graph RNA_nn changing from Graph to Graph Warning: Graph RNA_snn changing from Graph to Graph Warning: DimReduc pca changing from DimReduc to DimReduc Warning: DimReduc umap changing from DimReduc to DimReduc Ensuring keys are in the proper structure Ensuring feature names don't have underscores or pipes Updating slots in RNA Updating slots in RNA_nn Setting default assay of RNA_nn to RNA Updating slots in RNA_snn Setting default assay of RNA_snn to RNA Updating slots in pca Updating slots in umap Setting umap DimReduc to global Setting assay used for NormalizeData.RNA to RNA Setting assay used for FindVariableFeatures.RNA to RNA Setting assay used for ScaleData.RNA to RNA Setting assay used for RunPCA.RNA to RNA Setting assay used for JackStraw.RNA.pca to RNA No assay information could be found for ScoreJackStraw Setting assay used for FindNeighbors.RNA.pca to RNA No assay information could be found for FindClusters Setting assay used for RunUMAP.RNA.pca to RNA Validating object structure for Assay ‘RNA’ Validating object structure for Graph ‘RNA_nn’ Validating object structure for Graph ‘RNA_snn’ Validating object structure for DimReduc ‘pca’ Validating object structure for DimReduc ‘umap’ Object representation is consistent with the most current Seurat version Warning messages: 1: Adding a command log without an assay associated with it 2: Adding a command log without an assay associated with it sessionInfo() R version 4.1.3 (2022-03-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

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

other attached packages: [1] Seurat_5.0.1 SeuratObject_5.0.1 sp_1.6-0 pbmc3k.SeuratData_3.1.4 SeuratData_0.2.2.9001

loaded via a namespace (and not attached): [1] Rtsne_0.16 ggbeeswarm_0.7.1 colorspace_2.1-0 deldir_1.0-6 ellipsis_0.3.2
[6] ggridges_0.5.4 snakecase_0.11.1 circlize_0.4.15 GlobalOptions_0.1.2 RcppHNSW_0.4.1
[11] rstudioapi_0.15.0 spatstat.data_3.0-1 scCustomize_2.0.1 leiden_0.4.3 listenv_0.9.0
[16] ggrepel_0.9.3 lubridate_1.9.2 RSpectra_0.16-1 fansi_1.0.4 codetools_0.2-19
[21] splines_4.1.3 polyclip_1.10-4 spam_2.9-1 jsonlite_1.8.4 ica_1.0-3
[26] cluster_2.1.4 png_0.1-8 uwot_0.1.14 ggprism_1.0.4 shiny_1.7.4.1
[31] sctransform_0.4.1 spatstat.sparse_3.0-1 compiler_4.1.3 httr_1.4.7 Matrix_1.6-4
[36] fastmap_1.1.1 lazyeval_0.2.2 cli_3.6.1 later_1.3.0 htmltools_0.5.4
[41] tools_4.1.3 igraph_1.4.2 dotCall64_1.0-2 gtable_0.3.4 glue_1.6.2
[46] RANN_2.6.1 reshape2_1.4.4 dplyr_1.1.2 rappdirs_0.3.3 Rcpp_1.0.10
[51] scattermore_1.2 vctrs_0.6.5 spatstat.explore_3.1-0 nlme_3.1-162 progressr_0.13.0
[56] lmtest_0.9-40 spatstat.random_3.1-4 stringr_1.5.1 globals_0.16.2 timechange_0.2.0
[61] mime_0.12 miniUI_0.1.1.1 lifecycle_1.0.4 irlba_2.3.5.1 goftest_1.2-3
[66] future_1.33.0 MASS_7.3-58.3 zoo_1.8-11 scales_1.2.1 promises_1.2.0.1
[71] spatstat.utils_3.0-2 parallel_4.1.3 rematch2_2.1.2 RColorBrewer_1.1-3 reticulate_1.28
[76] pbapply_1.7-2 gridExtra_2.3 ggplot2_3.4.4 ggrastr_1.0.1 stringi_1.7.12
[81] paletteer_1.5.0 fastDummies_1.7.3 shape_1.4.6 rlang_1.1.2 pkgconfig_2.0.3
[86] matrixStats_0.63.0 lattice_0.20-45 ROCR_1.0-11 purrr_1.0.2 tensor_1.5
[91] patchwork_1.1.3 htmlwidgets_1.6.2 cowplot_1.1.1 tidyselect_1.2.0 parallelly_1.36.0
[96] RcppAnnoy_0.0.20 plyr_1.8.8 magrittr_2.0.3 R6_2.5.1 generics_0.1.3
[101] pillar_1.9.0 fitdistrplus_1.1-11 survival_3.5-5 abind_1.4-5 tibble_3.2.1
[106] future.apply_1.11.0 crayon_1.5.2 janitor_2.2.0 KernSmooth_2.23-20 utf8_1.2.3
[111] spatstat.geom_3.1-0 plotly_4.10.1 grid_4.1.3 data.table_1.14.8 forcats_1.0.0
[116] digest_0.6.31 xtable_1.8-4 tidyr_1.3.0 httpuv_1.6.9 munsell_0.5.0
[121] beeswarm_0.4.0 viridisLite_0.4.2 vipor_0.4.5

what's wrong for it? Thank you!!!!

chuiqin commented 6 months ago

The sample data is an old version of Seurat object. When updating from an old version of Seurat object to a new version of Seurat object, there will be relevant information prompts. You can ignore it.