Issue when subsetting

[pabloatria18]

Hello Whenever I try to run this command: cds_subset <- cds[rowData(cds)$gene_short_name %in% Genes1,]

I get this error message:

Error: subscript is a NSBS object that is incompatible with the current subsetting operation

Here is my session info:

R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252

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

other attached packages: [1] SeuratWrappers_0.3.0 devtools_2.3.2 usethis_2.0.0 monocle3_0.2.3.0
[5] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.2
[9] IRanges_2.24.1 S4Vectors_0.28.1 MatrixGenerics_1.2.0 matrixStats_0.57.0
[13] Biobase_2.50.0 BiocGenerics_0.36.0 sctransform_0.3.2 forcats_0.5.0
[17] stringr_1.4.0 purrr_0.3.4 readr_1.4.0 tidyr_1.1.2
[21] tibble_3.0.5 tidyverse_1.3.0 ggplot2_3.3.3 dplyr_1.0.3
[25] patchwork_1.1.1 cowplot_1.1.1 Seurat_3.9.9.9027 glmGamPoi_1.2.0

loaded via a namespace (and not attached): [1] utf8_1.1.4 reticulate_1.18 tidyselect_1.1.0 htmlwidgets_1.5.3
[5] grid_4.0.3 Rtsne_0.15 munsell_0.5.0 codetools_0.2-16
[9] ica_1.0-2 future_1.21.0 miniUI_0.1.1.1 withr_2.4.0
[13] colorspace_2.0-0 rstudioapi_0.13 ROCR_1.0-11 tensor_1.5
[17] listenv_0.8.0 labeling_0.4.2 GenomeInfoDbData_1.2.4 polyclip_1.10-0
[21] farver_2.0.3 rprojroot_2.0.2 parallelly_1.23.0 vctrs_0.3.6
[25] generics_0.1.0 xfun_0.19 R6_2.5.0 rsvd_1.0.3
[29] bitops_1.0-6 spatstat.utils_1.20-2 DelayedArray_0.16.0 assertthat_0.2.1
[33] promises_1.1.1 scales_1.1.1 gtable_0.3.0 globals_0.14.0
[37] processx_3.4.5 goftest_1.2-2 rlang_0.4.9 splines_4.0.3
[41] lazyeval_0.2.2 broom_0.7.3 BiocManager_1.30.10 reshape2_1.4.4
[45] abind_1.4-5 modelr_0.1.8 backports_1.2.1 httpuv_1.5.5
[49] tools_4.0.3 ellipsis_0.3.1 RColorBrewer_1.1-2 proxy_0.4-24
[53] sessioninfo_1.1.1 ggridges_0.5.3 Rcpp_1.0.6 plyr_1.8.6
[57] sparseMatrixStats_1.2.0 zlibbioc_1.36.0 RCurl_1.98-1.2 ps_1.5.0
[61] prettyunits_1.1.1 rpart_4.1-15 deldir_0.2-9 pbapply_1.4-3
[65] viridis_0.5.1 zoo_1.8-8 haven_2.3.1 ggrepel_0.9.1
[69] cluster_2.1.0 fs_1.5.0 tinytex_0.28 magrittr_2.0.1
[73] data.table_1.13.6 RSpectra_0.16-0 scattermore_0.7 lmtest_0.9-38
[77] reprex_0.3.0 RANN_2.6.1 fitdistrplus_1.1-3 pkgload_1.1.0
[81] hms_1.0.0 mime_0.9 xtable_1.8-4 readxl_1.3.1
[85] gridExtra_2.3 testthat_3.0.0 compiler_4.0.3 KernSmooth_2.23-17
[89] crayon_1.3.4 htmltools_0.5.1 mgcv_1.8-33 later_1.1.0.1
[93] lubridate_1.7.9.2 DBI_1.1.1 dbplyr_2.0.0 MASS_7.3-53
[97] leidenbase_0.1.2 Matrix_1.3-2 cli_2.2.0 igraph_1.2.6
[101] pkgconfig_2.0.3 plotly_4.9.3 xml2_1.3.2 XVector_0.30.0
[105] rvest_0.3.6 callr_3.5.1 digest_0.6.27 RcppAnnoy_0.0.18
[109] spatstat.data_1.7-0 cellranger_1.1.0 leiden_0.3.6 uwot_0.1.10
[113] DelayedMatrixStats_1.12.2 shiny_1.5.0 lifecycle_0.2.0 nlme_3.1-149
[117] jsonlite_1.7.2 desc_1.2.0 viridisLite_0.3.0 limma_3.46.0
[121] fansi_0.4.1 pillar_1.4.7 lattice_0.20-41 fastmap_1.0.1
[125] httr_1.4.2 pkgbuild_1.2.0 survival_3.2-7 glue_1.4.2
[129] remotes_2.2.0 spatstat_1.64-1 png_0.1-7 stringi_1.5.3
[133] memoise_1.1.0 irlba_2.3.3 future.apply_1.7.0

[brgew]

Hi,

Could you check whether rowData(cds)$gene_short_name gives a list of short gene names?

[EugeneEA]

@brgew Hi , I have the same issue and in my case rowData(cds)$gene_short_name, produces the list of names, Best, Eugene