Closed Sara-Tavallaei closed 3 months ago
Hi,
Thank you for taking the time to write this issue. We have seen this issue before and have since resolved in in the latest version of hdWGCNA. Please install the latest version and run your code again.
Hi,
Thank you for taking the time to write this issue. We have seen this issue before and have since resolved in in the latest version of hdWGCNA. Please install the latest version and run your code again.
Thanks! It worked.
Best regards!
Hi!
while using "ModuleEigengenes" function in hdWGCNA analysis on single-cell RNA-seq data, I face the following error:
seurat_obj <- ModuleEigengenes(seurat_obj = seurat_obj, group.by.vars = 'DataSet', wgcna_name = 'GBM_PBMC')
Error in !CheckWGCNAName(seurat_obj, wgcna_name) : invalid argument type
I don't understand what's the reason behind this error. Could you help me solve it?
In the following, I attach the previous steps:
Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
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/Tehran tzcode source: system (glibc)
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] hdWGCNA_0.3.00 igraph_2.0.2 ggrepel_0.9.5
[4] harmony_1.2.0 Rcpp_1.0.12 WGCNA_1.72-5
[7] fastcluster_1.2.6 dynamicTreeCut_1.63-1 patchwork_1.2.0
[10] cowplot_1.1.3 lubridate_1.9.3 forcats_1.0.0
[13] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
[16] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[19] ggplot2_3.4.4 tidyverse_2.0.0 SeuratObject_4.1.4
[22] Seurat_4.4.0
loaded via a namespace (and not attached): [1] RcppAnnoy_0.0.22 splines_4.3.2 later_1.3.2
[4] bitops_1.0-7 polyclip_1.10-6 preprocessCore_1.62.1
[7] rpart_4.1.21 lifecycle_1.0.4 doParallel_1.0.17
[10] globals_0.16.2 lattice_0.21-9 MASS_7.3-60
[13] backports_1.4.1 magrittr_2.0.3 rmarkdown_2.25
[16] Hmisc_5.1-1 plotly_4.10.4 httpuv_1.6.14
[19] sctransform_0.4.1 spam_2.10-0 sp_2.1-3
[22] spatstat.sparse_3.0-3 reticulate_1.35.0 pbapply_1.7-2
[25] DBI_1.2.2 RColorBrewer_1.1-3 abind_1.4-7
[28] zlibbioc_1.46.0 Rtsne_0.17 BiocGenerics_0.46.0
[31] RCurl_1.98-1.14 nnet_7.3-19 GenomeInfoDbData_1.2.10 [34] IRanges_2.34.1 S4Vectors_0.38.2 irlba_2.3.5.1
[37] listenv_0.9.1 spatstat.utils_3.0-4 goftest_1.2-3
[40] spatstat.random_3.2-2 fitdistrplus_1.1-11 parallelly_1.37.0
[43] leiden_0.4.3.1 codetools_0.2-19 tidyselect_1.2.0
[46] farver_2.1.1 tester_0.2.0 matrixStats_1.2.0
[49] stats4_4.3.2 base64enc_0.1-4 spatstat.explore_3.2-6 [52] jsonlite_1.8.8 ellipsis_0.3.2 progressr_0.14.0
[55] Formula_1.2-6 ggridges_0.5.6 survival_3.5-8
[58] iterators_1.0.14 foreach_1.5.2 tools_4.3.2
[61] ica_1.0-3 glue_1.7.0 gridExtra_2.3
[64] xfun_0.42 GenomeInfoDb_1.36.4 withr_3.0.0
[67] fastmap_1.1.1 fansi_1.0.6 digest_0.6.34
[70] timechange_0.3.0 R6_2.5.1 mime_0.12
[73] colorspace_2.1-1 scattermore_1.2 GO.db_3.17.0
[76] tensor_1.5 spatstat.data_3.0-4 RSQLite_2.3.5
[79] utf8_1.2.4 generics_0.1.3 data.table_1.15.0
[82] FNN_1.1.4 httr_1.4.7 htmlwidgets_1.6.4
[85] uwot_0.1.16 pkgconfig_2.0.3 gtable_0.3.4
[88] blob_1.2.4 impute_1.74.1 lmtest_0.9-40
[91] XVector_0.40.0 htmltools_0.5.7 dotCall64_1.1-1
[94] scales_1.3.0 Biobase_2.60.0 png_0.1-8
[97] knitr_1.45 rstudioapi_0.15.0 tzdb_0.4.0
[100] reshape2_1.4.4 checkmate_2.3.1 nlme_3.1-164
[103] proxy_0.4-27 zoo_1.8-13 cachem_1.0.8
[106] KernSmooth_2.23-22 parallel_4.3.2 miniUI_0.1.1.1
[109] foreign_0.8-86 AnnotationDbi_1.62.2 pillar_1.9.0
[112] grid_4.3.2 vctrs_0.6.5 RANN_2.6.1
[115] promises_1.2.1 xtable_1.8-6 cluster_2.1.4
[118] htmlTable_2.4.2 evaluate_0.23 cli_3.6.2
[121] compiler_4.3.2 rlang_1.1.3 crayon_1.5.2
[124] future.apply_1.11.1 labeling_0.4.3 plyr_1.8.9
[127] stringi_1.8.3 viridisLite_0.4.2 deldir_2.0-2
[130] munsell_0.5.0 Biostrings_2.68.1 lazyeval_0.2.2
[133] spatstat.geom_3.2-8 Matrix_1.6-5 hms_1.1.3
[136] bit64_4.0.5 future_1.33.1 KEGGREST_1.40.1
[139] shiny_1.8.0 ROCR_1.0-11 memoise_2.0.1
[142] bit_4.0.5