Got errors when running tutorial, "error in evaluating the argument 'x' in selecting a method for function 'as.matrix': no slot of name "data" for this object of class "Assay5"" #41
Description
Dear authors,
I got an error message when I try to run the tutorial, Effect of Tal1 knock out on mouse development.
The error comes from the following code:
modules_wgcna = suppressMessages(get_wgcna_modules(convert_de_stat(de_stat) , n_hoods_sig.thresh = 4))The error is
Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'as.matrix': no slot of name "data" for this object of class "Assay5"
Traceback:
1. suppressMessages(get_wgcna_modules(convert_de_stat(de_stat),
. n_hoods_sig.thresh = 4))
2. withCallingHandlers(expr, message = function(c) if (inherits(c,
. classes)) tryInvokeRestart("muffleMessage"))
3. get_wgcna_modules(convert_de_stat(de_stat), n_hoods_sig.thresh = 4)
4. as.matrix(obj.seurat[["RNA"]]@data) # at line 44 of file <text>
5. .handleSimpleError(function (cond)
. .Internal(C_tryCatchHelper(addr, 1L, cond)), "no slot of name \"data\" for this object of class \"Assay5\"",
. base::quote(as.matrix(obj.seurat[["RNA"]]@data))) # at line 44 of file <text>
6. h(simpleError(msg, call))My sessionInfo is
R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] reshape2_1.4.4 scWGCNA_1.0.0
[3] viridis_0.6.5 viridisLite_0.4.2
[5] miloDE_0.0.0.9000 patchwork_1.2.0
[7] dplyr_1.1.4 scran_1.30.2
[9] scater_1.30.1 ggplot2_3.5.1
[11] scuttle_1.12.0 miloR_1.10.0
[13] edgeR_4.0.16 limma_3.58.1
[15] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0
[17] Biobase_2.62.0 GenomicRanges_1.54.1
[19] GenomeInfoDb_1.38.8 IRanges_2.36.0
[21] S4Vectors_0.40.2 BiocGenerics_0.48.1
[23] MatrixGenerics_1.14.0 matrixStats_1.3.0
[25] Seurat_5.1.0 SeuratObject_5.0.2
[27] sp_2.1-4
loaded via a namespace (and not attached):
[1] spatstat.sparse_3.1-0 bitops_1.0-7
[3] lubridate_1.9.3 doParallel_1.0.17
[5] httr_1.4.7 RColorBrewer_1.1-3
[7] dynamicTreeCut_1.63-1 repr_1.1.7
[9] backports_1.5.0 tools_4.3.3
[11] sctransform_0.4.1 utf8_1.2.4
[13] R6_2.5.1 lazyeval_0.2.2
[15] uwot_0.2.2 yardstick_1.3.1
[17] withr_3.0.0 gridExtra_2.3
[19] preprocessCore_1.64.0 progressr_0.14.0
[21] WGCNA_1.72-5 cli_3.6.3
[23] Cairo_1.6-2 spatstat.explore_3.3-1
[25] fastDummies_1.7.3 labeling_0.4.3
[27] spatstat.data_3.1-2 RcppGreedySetCover_0.1.0
[29] randomForest_4.7-1.1 ggridges_0.5.6
[31] pbapply_1.7-2 pbdZMQ_0.3-11
[33] foreign_0.8-87 dichromat_2.0-0.1
[35] parallelly_1.37.1 maps_3.4.2
[37] impute_1.76.0 rstudioapi_0.16.0
[39] RSQLite_2.3.7 pals_1.8
[41] generics_0.1.3 gtools_3.9.5
[43] ica_1.0-3 spatstat.random_3.3-1
[45] car_3.1-2 GO.db_3.18.0
[47] Matrix_1.6-5 ggbeeswarm_0.7.2
[49] fansi_1.0.6 abind_1.4-5
[51] lifecycle_1.0.4 carData_3.0-5
[53] recipes_1.1.0 SparseArray_1.2.4
[55] Rtsne_0.17 blob_1.2.4
[57] grid_4.3.3 promises_1.3.0
[59] dqrng_0.4.1 crayon_1.5.3
[61] miniUI_0.1.1.1 lattice_0.22-6
[63] beachmat_2.18.1 cowplot_1.1.3
[65] KEGGREST_1.42.0 mapproj_1.2.11
[67] knitr_1.48 pillar_1.9.0
[69] metapod_1.10.1 future.apply_1.11.2
[71] codetools_0.2-20 Augur_1.0.3
[73] leiden_0.4.3.1 glue_1.7.0
[75] rsample_1.2.1 spatstat.univar_3.0-0
[77] data.table_1.15.4 vctrs_0.6.5
[79] png_0.1-8 spam_2.10-0
[81] gtable_0.3.5 cachem_1.1.0
[83] xfun_0.45 gower_1.0.1
[85] S4Arrays_1.2.1 mime_0.12
[87] prodlim_2024.06.25 tidygraph_1.3.1
[89] survival_3.7-0 timeDate_4032.109
[91] iterators_1.0.14 pbmcapply_1.5.1
[93] hardhat_1.4.0 lava_1.8.0
[95] statmod_1.5.0 bluster_1.12.0
[97] fitdistrplus_1.2-1 ROCR_1.0-11
[99] ipred_0.9-14 nlme_3.1-165
[101] bit64_4.0.5 RcppAnnoy_0.0.22
[103] irlba_2.3.5.1 vipor_0.4.7
[105] KernSmooth_2.23-24 rpart_4.1.23
[107] Hmisc_5.1-3 DBI_1.2.3
[109] colorspace_2.1-0 nnet_7.3-19
[111] tidyselect_1.2.1 bit_4.0.5
[113] compiler_4.3.3 htmlTable_2.4.2
[115] BiocNeighbors_1.20.2 DelayedArray_0.28.0
[117] plotly_4.10.4 checkmate_2.3.1
[119] scales_1.3.0 lmtest_0.9-40
[121] stringr_1.5.1 digest_0.6.36
[123] goftest_1.2-3 spatstat.utils_3.0-5
[125] rmarkdown_2.27 XVector_0.42.0
[127] htmltools_0.5.8.1 pkgconfig_2.0.3
[129] base64enc_0.1-3 sparseMatrixStats_1.14.0
[131] fastmap_1.2.0 rlang_1.1.4
[133] htmlwidgets_1.6.4 shiny_1.8.1.1
[135] DelayedMatrixStats_1.24.0 farver_2.1.2
[137] zoo_1.8-12 jsonlite_1.8.8
[139] BiocParallel_1.36.0 BiocSingular_1.18.0
[141] RCurl_1.98-1.16 magrittr_2.0.3
[143] Formula_1.2-5 GenomeInfoDbData_1.2.11
[145] dotCall64_1.1-1 IRkernel_1.3.2
[147] munsell_0.5.1 Rcpp_1.0.12
[149] reticulate_1.38.0 furrr_0.3.1
[151] stringi_1.8.4 ggraph_2.2.1
[153] zlibbioc_1.48.2 MASS_7.3-60.0.1
[155] plyr_1.8.9 parallel_4.3.3
[157] listenv_0.9.1 ggrepel_0.9.5
[159] deldir_2.0-4 Biostrings_2.70.3
[161] graphlayouts_1.1.1 IRdisplay_1.1
[163] splines_4.3.3 tensor_1.5
[165] locfit_1.5-9.10 fastcluster_1.2.6
[167] ggpubr_0.6.0 igraph_2.0.3
[169] uuid_1.2-0 spatstat.geom_3.3-2
[171] ggsignif_0.6.4 RcppHNSW_0.6.0
[173] parsnip_1.2.1 ScaledMatrix_1.10.0
[175] evaluate_0.24.0 tester_0.2.0
[177] foreach_1.5.2 tweenr_2.0.3
[179] httpuv_1.6.15 RANN_2.6.1
[181] tidyr_1.3.1 purrr_1.0.2
[183] polyclip_1.10-6 future_1.33.2
[185] scattermore_1.2 ggforce_0.4.2
[187] rsvd_1.0.5 broom_1.0.6
[189] xtable_1.8-4 RSpectra_0.16-1
[191] rstatix_0.7.2 later_1.3.2
[193] class_7.3-22 tibble_3.2.1
[195] AnnotationDbi_1.64.1 memoise_2.0.1
[197] beeswarm_0.4.0 cluster_2.1.6
[199] timechange_0.3.0 globals_0.16.3
Dear authors, can you give me some advice on why this error occurs and how to fix it? Thanks.