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msraredon / NICHES

Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
https://msraredon.github.io/NICHES/
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Error in validObject(object = object) : invalid class “Assay5” object: Layers must be two-dimensional objects #42

Open pushpinder-bu opened 3 months ago

pushpinder-bu commented 3 months ago

Hi,

I am running NICHES on a seurat object version ‘5.0.2’ and have been getting the below error. Any suggestions?

Error in validObject(object = object) : invalid class “Assay5” object: Layers must be two-dimensional objects

sessionInfo() R version 4.2.3 (2023-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: AlmaLinux 8.10 (Cerulean Leopard)

Matrix products: default BLAS: /share/pkg.7/r/4.2.3/install/lib64/R/lib/libRblas.so LAPACK: /share/pkg.7/r/4.2.3/install/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] RColorBrewer_1.1-3 writexl_1.5.0 ggbeeswarm_0.7.1 TSCAN_1.36.0
[5] TrajectoryUtils_1.6.0 SingleCellExperiment_1.20.1 SummarizedExperiment_1.28.0 Biobase_2.58.0
[9] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9 IRanges_2.32.0 S4Vectors_0.36.2
[13] BiocGenerics_0.44.0 MatrixGenerics_1.10.0 matrixStats_1.1.0 igraph_2.0.3
[17] gridExtra_2.3 ggthemes_5.1.0 ComplexHeatmap_2.14.0 cowplot_1.1.3
[21] Connectome_1.0.1 ggplot2_3.5.1 dplyr_1.1.4 NICHES_1.1.0
[25] SeuratWrappers_0.3.5 pbmcMultiome.SeuratData_0.1.4 SeuratData_0.2.2.9001 Seurat_5.1.0
[29] SeuratObject_5.0.2 sp_2.1-4 future_1.33.2 devtools_2.4.5
[33] usethis_2.1.6

loaded via a namespace (and not attached): [1] rappdirs_0.3.3 scattermore_1.2 R.methodsS3_1.8.2 ragg_1.2.5 tidyr_1.3.1
[6] bit64_4.0.5 knitr_1.47 irlba_2.3.5.1 DelayedArray_0.24.0 R.utils_2.12.3
[11] data.table_1.15.4 RCurl_1.98-1.14 doParallel_1.0.17 generics_0.1.3 callr_3.7.3
[16] RANN_2.6.1 combinat_0.0-8 bit_4.0.5 tzdb_0.3.0 xml2_1.3.3
[21] lubridate_1.9.2 spatstat.data_3.0-4 httpuv_1.6.15 xfun_0.44 hms_1.1.2
[26] evaluate_0.23 promises_1.3.0 progress_1.2.2 fansi_1.0.6 caTools_1.18.2
[31] readxl_1.4.2 htmlwidgets_1.6.4 spatstat.geom_3.2-9 purrr_1.0.2 ellipsis_0.3.2
[36] selectr_0.4-2 RSpectra_0.16-1 backports_1.4.1 deldir_2.0-4 vctrs_0.6.5
[41] remotes_2.5.0 ROCR_1.0-11 abind_1.4-7 cachem_1.1.0 withr_3.0.0
[46] progressr_0.14.0 vroom_1.6.1 checkmate_2.1.0 sctransform_0.4.1 prettyunits_1.1.1
[51] mclust_6.0.0 goftest_1.2-3 cluster_2.1.4 dotCall64_1.1-1 lazyeval_0.2.2
[56] crayon_1.5.2 spatstat.explore_3.2-7 pkgconfig_2.0.3 labeling_0.4.3 nlme_3.1-162
[61] vipor_0.4.5 pkgload_1.3.2 rlang_1.1.4 globals_0.16.3 lifecycle_1.0.4
[66] miniUI_0.1.1.1 fastDummies_1.7.3 rsvd_1.0.5 cellranger_1.1.0 rprojroot_2.0.4
[71] polyclip_1.10-6 RcppHNSW_0.6.0 lmtest_0.9-40 Matrix_1.6-5 zoo_1.8-12
[76] beeswarm_0.4.0 ggridges_0.5.6 GlobalOptions_0.1.2 processx_3.8.0 png_0.1-8
[81] viridisLite_0.4.2 rjson_0.2.21 bitops_1.0-7 R.oo_1.26.0 KernSmooth_2.23-20
[86] spam_2.10-0 Biostrings_2.66.0 shape_1.4.6 stringr_1.5.1 parallelly_1.37.1
[91] spatstat.random_3.2-3 readr_2.1.4 scales_1.3.0 memoise_2.0.1 magrittr_2.0.3
[96] plyr_1.8.9 ica_1.0-3 gplots_3.1.3.1 zlibbioc_1.44.0 compiler_4.2.3
[101] clue_0.3-64 fitdistrplus_1.1-11 Rsamtools_2.14.0 cli_3.6.2 XVector_0.38.0
[106] urlchecker_1.0.1 listenv_0.9.1 patchwork_1.2.0.9000 pbapply_1.7-2 ps_1.7.2
[111] MASS_7.3-58.3 mgcv_1.8-42 tidyselect_1.2.1 stringi_1.8.4 textshaping_0.3.6
[116] yaml_2.3.8 ggrepel_0.9.5 timechange_0.2.0 fastmatch_1.1-3 tools_4.2.3
[121] future.apply_1.11.2 parallel_4.2.3 circlize_0.4.15 rstudioapi_0.14 foreach_1.5.2
[126] farver_2.1.2 Rtsne_0.17 digest_0.6.35 BiocManager_1.30.23 shiny_1.8.1.1
[131] Rcpp_1.0.12 later_1.3.2 RcppAnnoy_0.0.22 httr_1.4.7 colorspace_2.1-1
[136] rvest_1.0.3 XML_3.99-0.16.1 fs_1.6.4 tensor_1.5 reticulate_1.37.0
[141] splines_4.2.3 uwot_0.2.2 RcppRoll_0.3.0 OmnipathR_3.13.5 spatstat.utils_3.1-0
[146] plotly_4.10.4 sessioninfo_1.2.2 systemfonts_1.0.4 xtable_1.8-6 jsonlite_1.8.8
[151] R6_2.5.1 profvis_0.3.7 pillar_1.9.0 htmltools_0.5.8.1 mime_0.12
[156] glue_1.7.0 fastmap_1.2.0 BiocParallel_1.32.6 ggmin_0.0.0.9000 codetools_0.2-19
[161] pkgbuild_1.4.0 Signac_1.13.0 utf8_1.2.4 logger_0.3.0 lattice_0.20-45
[166] spatstat.sparse_3.0-3 tibble_3.2.1 curl_5.2.1 leiden_0.4.3.1 gtools_3.9.5
[171] zip_2.2.2 openxlsx_4.2.5.2 survival_3.5-5 rmarkdown_2.27 desc_1.4.2
[176] fastICA_1.2-3 munsell_0.5.1 GetoptLong_1.0.5 GenomeInfoDbData_1.2.9 iterators_1.0.14
[181] reshape2_1.4.4 gtable_0.3.5