Question about [my question]Error in !CheckWGCNAName(seurat_obj, wgcna_name) : invalid argument type

[RGT183]

When I used ModuleEigengenes, the questtion is this
seurat_obj <- ModuleEigengenes(

• seurat_obj,
• group.by.vars="sample"
• )
  Error in !CheckWGCNAName(seurat_obj, wgcna_name) : invalid argument type
  Then, I re-install the package and try, also don't work
  sessionInfo()
  R version 4.4.2 (2024-10-31 ucrt)
  Platform: x86_64-w64-mingw32/x64
  Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8
[2] LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] hdWGCNA_0.3.00 igraph_2.1.1 ggrepel_0.9.6
[4] harmony_1.2.1 Rcpp_1.0.13-1 WGCNA_1.73
[7] fastcluster_1.2.6 dynamicTreeCut_1.63-1 patchwork_1.3.0
[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_3.5.1 tidyverse_2.0.0 Seurat_5.1.0
[22] SeuratObject_5.0.2 sp_2.1-4

loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.4.2 later_1.3.2
[4] polyclip_1.10-7 preprocessCore_1.68.0 rpart_4.1.23
[7] fastDummies_1.7.4 lifecycle_1.0.4 doParallel_1.0.17
[10] globals_0.16.3 lattice_0.22-6 MASS_7.3-61
[13] backports_1.5.0 magrittr_2.0.3 rmarkdown_2.29
[16] Hmisc_5.2-0 plotly_4.10.4 remotes_2.5.0
[19] httpuv_1.6.15 sctransform_0.4.1 spam_2.11-0
[22] sessioninfo_1.2.2 pkgbuild_1.4.5 spatstat.sparse_3.1-0
[25] reticulate_1.39.0 pbapply_1.7-2 DBI_1.2.3
[28] RColorBrewer_1.1-3 zlibbioc_1.52.0 abind_1.4-8
[31] pkgload_1.4.0 Rtsne_0.17 BiocGenerics_0.52.0
[34] nnet_7.3-19 GenomeInfoDbData_1.2.13 IRanges_2.40.0
[37] S4Vectors_0.44.0 irlba_2.3.5.1 listenv_0.9.1
[40] spatstat.utils_3.1-1 goftest_1.2-3 RSpectra_0.16-2
[43] spatstat.random_3.3-2 fitdistrplus_1.2-1 parallelly_1.39.0
[46] commonmark_1.9.2 leiden_0.4.3.1 codetools_0.2-20
[49] xml2_1.3.6 tidyselect_1.2.1 UCSC.utils_1.2.0
[52] farver_2.1.2 tester_0.2.0 base64enc_0.1-3
[55] matrixStats_1.4.1 stats4_4.4.2 spatstat.explore_3.3-3
[58] jsonlite_1.8.9 Formula_1.2-5 ellipsis_0.3.2
[61] progressr_0.15.0 ggridges_0.5.6 survival_3.7-0
[64] iterators_1.0.14 foreach_1.5.2 tools_4.4.2
[67] ica_1.0-3 glue_1.8.0 gridExtra_2.3
[70] xfun_0.49 usethis_3.0.0 GenomeInfoDb_1.42.0
[73] withr_3.0.2 BiocManager_1.30.25 fastmap_1.2.0
[76] fansi_1.0.6 digest_0.6.37 timechange_0.3.0
[79] R6_2.5.1 mime_0.12 colorspace_2.1-1
[82] scattermore_1.2 GO.db_3.20.0 tensor_1.5
[85] spatstat.data_3.1-2 RSQLite_2.3.7 RhpcBLASctl_0.23-42
[88] utf8_1.2.4 generics_0.1.3 data.table_1.16.2
[91] FNN_1.1.4.1 httr_1.4.7 htmlwidgets_1.6.4
[94] uwot_0.2.2 pkgconfig_2.0.3 gtable_0.3.6
[97] blob_1.2.4 impute_1.80.0 lmtest_0.9-40
[100] XVector_0.46.0 htmltools_0.5.8.1 profvis_0.4.0
[103] dotCall64_1.2 scales_1.3.0 Biobase_2.66.0
[106] png_0.1-8 spatstat.univar_3.1-1 knitr_1.49
[109] rstudioapi_0.17.1 tzdb_0.4.0 reshape2_1.4.4
[112] checkmate_2.3.2 nlme_3.1-166 curl_6.0.0
[115] proxy_0.4-27 cachem_1.1.0 zoo_1.8-12
[118] KernSmooth_2.23-24 parallel_4.4.2 miniUI_0.1.1.1
[121] foreign_0.8-87 AnnotationDbi_1.68.0 pillar_1.9.0
[124] grid_4.4.2 vctrs_0.6.5 RANN_2.6.2
[127] urlchecker_1.0.1 promises_1.3.0 xtable_1.8-4
[130] cluster_2.1.6 htmlTable_2.4.3 evaluate_1.0.1
[133] cli_3.6.3 compiler_4.4.2 rlang_1.1.4
[136] crayon_1.5.3 future.apply_1.11.3 labeling_0.4.3
[139] plyr_1.8.9 fs_1.6.5 stringi_1.8.4
[142] viridisLite_0.4.2 deldir_2.0-4 munsell_0.5.1
[145] Biostrings_2.74.0 lazyeval_0.2.2 devtools_2.4.5
[148] spatstat.geom_3.3-3 Matrix_1.7-1 RcppHNSW_0.6.0
[151] hms_1.1.3 bit64_4.5.2 future_1.34.0
[154] KEGGREST_1.46.0 shiny_1.9.1 ROCR_1.0-11
[157] memoise_2.0.1 bit_4.5.0

[smorabit]

Can you please update hdWGCNA to the latest version and run it again?

[Clapton9527]

Hi! I have the same problem

RNA <- ModuleEigengenes( RNA, group.by.vars="orig.ident" )
Error in !CheckWGCNAName(seurat_obj, wgcna_name) : invalid argument type

sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Asia/Shanghai
tzcode source: system (glibc)

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

other attached packages:
[1] hdWGCNA_0.4.00 igraph_1.5.1 WGCNA_1.73
[4] fastcluster_1.2.3 dynamicTreeCut_1.63-1 scran_1.28.2
[7] scater_1.28.0 scuttle_1.10.2 scales_1.2.1
[10] miloR_1.8.1 edgeR_3.42.4 limma_3.56.2
[13] GSEABase_1.62.0 graph_1.78.0 annotate_1.78.0
[16] XML_3.99-0.14 GSVA_1.48.3 pheatmap_1.0.12
[19] gplots_3.1.3 ggstatsplot_0.12.0 survminer_0.4.9
[22] survival_3.5-7 COSG_0.9.0 tinyarray_2.4.2
[25] msigdbr_7.5.1 TCGAbiolinks_2.28.3 circlize_0.4.15
[28] RColorBrewer_1.1-3 ComplexHeatmap_2.16.0 tictoc_1.2
[31] Startrac_0.1.0 viridis_0.6.4 viridisLite_0.4.2
[34] ggpubr_0.6.0 ggrepel_0.9.3 sscVis_0.1.0
[37] SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.2 GenomicRanges_1.52.0
[40] GenomeInfoDb_1.36.3 MatrixGenerics_1.12.3 matrixStats_1.0.0
[43] plyr_1.8.8 data.table_1.14.8 clusterProfiler_4.8.3
[46] org.Hs.eg.db_3.17.0 AnnotationDbi_1.62.2 IRanges_2.34.1
[49] S4Vectors_0.38.1 ClusterGVis_0.1.1 monocle_2.28.0
[52] DDRTree_0.1.5 irlba_2.3.5.1 VGAM_1.1-8
[55] Biobase_2.60.0 BiocGenerics_0.46.0 Matrix_1.6-1
[58] scRNAtoolVis_0.0.7 lubridate_1.9.2 forcats_1.0.0
[61] purrr_1.0.2 tidyr_1.3.0 tibble_3.2.1
[64] tidyverse_2.0.0 qs_0.27.2 readr_2.1.4
[67] reshape2_1.4.4 patchwork_1.1.3 dplyr_1.1.3
[70] clustree_0.5.0 ggraph_2.1.0 harmony_1.2.1
[73] Rcpp_1.0.11 stringr_1.5.0 magrittr_2.0.3
[76] cowplot_1.1.1 ggplot2_3.4.3 SeuratObject_4.1.3
[79] Seurat_4.3.0.1

loaded via a namespace (and not attached):
[1] DBI_1.1.3 httr_1.4.7 BiocParallel_1.34.2
[4] prettyunits_1.1.1 yulab.utils_0.0.9 ggplotify_0.1.2
[7] sparseMatrixStats_1.12.2 spatstat.geom_3.2-5 babelgene_22.9
[10] survMisc_0.5.6 pillar_1.9.0 R6_2.5.1
[13] boot_1.3-28.1 mime_0.12 correlation_0.8.4
[16] reticulate_1.31 uwot_0.1.16 Rhdf5lib_1.22.0
[19] libcoin_1.0-9 ROCR_1.0-11 Hmisc_5.1-0
[22] rprojroot_2.0.3 fields_15.2 downloader_0.4
[25] KMsurv_0.1-5 parallelly_1.36.0 GlobalOptions_0.1.2
[28] sparsesvd_0.2-2 FNN_1.1.3.2 caTools_1.18.2
[31] polyclip_1.10-4 beachmat_2.16.0 htmltools_0.5.6
[34] fansi_1.0.4 lambda.r_1.2.4 remotes_2.4.2.1
[37] datawizard_0.8.0 fastICA_1.2-3 car_3.1-2
[40] stringfish_0.16.0 fgsea_1.26.0 spatstat.utils_3.1-0
[43] HDO.db_0.99.1 maps_3.4.1 rpart_4.1.19
[46] clue_0.3-64 qlcMatrix_0.9.7 scatterpie_0.2.1
[49] fitdistrplus_1.1-11 goftest_1.2-3 tidyselect_1.2.0
[52] RSQLite_2.3.1 GenomeInfoDbData_1.2.10 utf8_1.2.3
[55] ScaledMatrix_1.8.1 scattermore_1.2 sessioninfo_1.2.2
[58] spatstat.data_3.0-1 gridExtra_2.3 fs_1.6.3
[61] rvest_1.0.3 sctransform_0.4.1 future.apply_1.11.0
[64] vipor_0.4.5 Rtsne_0.16 DelayedMatrixStats_1.22.6
[67] TCGAbiolinksGUI.data_1.20.0 lazyeval_0.2.2 carData_3.0-5
[70] munsell_0.5.0 treeio_1.24.3 profvis_0.3.8
[73] pracma_2.4.2 bitops_1.0-7 labeling_0.4.3
[76] KEGGREST_1.40.0 promises_1.2.1 shape_1.4.6
[79] rhdf5filters_1.12.1 terra_1.7-46 zoo_1.8-12
[82] locfit_1.5-9.8 DelayedArray_0.26.7 multcomp_1.4-25
[85] paletteer_1.5.0 tools_4.3.1 ape_5.7-1
[88] processx_3.8.2 insight_0.19.3 shiny_1.7.5
[91] BiocFileCache_2.8.0 rlang_1.1.1 generics_0.1.3
[94] BiocSingular_1.16.0 ggridges_0.5.4 MetaGxBreast_1.20.0
[97] evaluate_0.21 bayestestR_0.13.1 devtools_2.4.5
[100] colorspace_2.1-0 ellipsis_0.3.2 withr_2.5.0
[103] RCurl_1.98-1.12 futile.logger_1.4.3 statsExpressions_1.5.1
[106] xtable_1.8-4 lme4_1.1-34 aplot_0.2.0
[109] ks_1.14.1 mclust_6.0.0 httpuv_1.6.11
[112] copykat_1.1.0 rmarkdown_2.24 metapod_1.8.0
[115] MASS_7.3-60 dqrng_0.3.1 docopt_0.7.1
[118] broom_1.0.5 deldir_1.0-9 GO.db_3.17.0
[121] sandwich_3.0-2 rhdf5_2.44.0 tensor_1.5
[124] vctrs_0.6.3 lifecycle_1.0.3 proxy_0.4-27
[127] codetools_0.2-19 nlme_3.1-163 combinat_0.0-8
[130] future_1.33.0 progress_1.2.2 dbplyr_2.3.3
[133] pkgload_1.3.2.1 rstudioapi_0.15.0 stringi_1.7.12
[136] hms_1.1.3 pbapply_1.7-2 minqa_1.2.5
[139] tester_0.1.7 cachem_1.0.8 BiocManager_1.30.22
[142] tidytree_0.4.5 listenv_0.9.0 XVector_0.40.0
[145] ggrastr_1.0.2 urlchecker_1.0.1 plotly_4.10.2
[148] ggtree_3.8.2 enrichplot_1.20.1 ExperimentHub_2.8.1
[151] GetoptLong_1.0.5 pkgbuild_1.4.2 ggfun_0.1.2
[154] HDF5Array_1.28.1 ggsci_3.0.0 htmlwidgets_1.6.2
[157] Formula_1.2-5 interactiveDisplayBase_1.38.0 dendextend_1.17.1
[160] memoise_2.0.1 crayon_1.5.2 gridGraphics_0.5-1
[163] rappdirs_0.3.3 S4Arrays_1.0.6 xml2_1.3.5
[166] filelock_1.0.2 preprocessCore_1.62.1 GOSemSim_2.26.1
[169] png_0.1-8 progressr_0.14.0 tzdb_0.4.0
[172] emmeans_1.8.8 infercnv_1.16.0 fastmap_1.1.1
[175] coda_0.19-4 tidygraph_1.2.3 pkgconfig_2.0.3
[178] cli_3.6.1 beeswarm_0.4.0 DOSE_3.26.1
[181] ggforce_0.4.1 ps_1.7.5 ggsignif_0.6.4
[184] nnet_7.3-19 gridBase_0.4-7 zeallot_0.1.0
[187] ggalluvial_0.12.5 lmtest_0.9-40 BiocVersion_3.17.1
[190] usethis_2.2.2 RcppAnnoy_0.0.21 DoubletFinder_2.0.3
[193] argparse_2.2.2 slam_0.1-50 timechange_0.2.0
[196] rjags_4-14 ggdendro_0.1.23 foreign_0.8-84
[199] blob_1.2.4 impute_1.74.1 globals_0.16.2
[202] ggbeeswarm_0.7.2 knitr_1.43 ica_1.0-3
[205] spam_2.9-1 compiler_4.3.1 rjson_0.2.21
[208] RcppParallel_5.1.7 biomaRt_2.56.1 bit_4.0.5
[211] leidenbase_0.1.25 AnnotationHub_3.8.0 BiocNeighbors_1.18.0
[214] glue_1.6.2 sp_2.0-0 estimability_1.4.1
[217] formatR_1.14 parameters_0.21.1 digest_0.6.33
[220] leiden_0.4.3 graphlayouts_1.0.0 foreach_1.5.2
[223] RApiSerialize_0.1.4 spatstat.random_3.1-5 zlibbioc_1.46.0
[226] dotCall64_1.0-2 tweenr_2.0.2 lattice_0.21-8
[229] statmod_1.5.0 rsvd_1.0.5 gson_0.1.0
[232] nloptr_2.0.3 mvtnorm_1.2-3 yaml_2.3.7
[235] qvalue_2.32.0 later_1.3.1 modeltools_0.2-23
[238] backports_1.4.1 rstatix_0.7.2 moduleColor_1.8-4
[241] shadowtext_0.1.2 parallel_4.3.1 rematch2_2.1.2
[244] parallelDist_0.2.6 miniUI_0.1.1.1 gtable_0.3.4
[247] abind_1.4-5 xfun_0.40 Biostrings_2.68.1
[250] curl_5.0.2 callr_3.7.3 doParallel_1.0.17
[253] KernSmooth_2.23-22 futile.options_1.0.1 desc_1.4.2
[256] jsonlite_1.8.7 coin_1.4-2 base64enc_0.1-3
[259] monocle3_1.3.4 iterators_1.0.14 TH.data_1.1-2
[262] RhpcBLASctl_0.23-42 HSMMSingleCell_1.20.0 km.ci_0.5-6
[265] fastmatch_1.1-4 checkmate_2.2.0 gtools_3.9.4
[268] htmlTable_2.4.1 spatstat.sparse_3.0-2 RANN_2.6.1
[271] bluster_1.10.0 phyclust_0.1-34 spatstat.explore_3.2-3
[274] bit64_4.0.5 cluster_2.1.4 farver_2.1.1
[277] org.Mm.eg.db_3.17.0

And I installed the latest version of hdWCGNA as mentioned above hdWGCNA_0.4.00 and run it again.
However, the same problem happened again

[reJELIN]

I'm encoutering the same error at the same step:

Error in !CheckWGCNAName(seurat_obj, wgcna_name) : invalid argument type

i'm with seurat v5 and the last update of your package (0.4.0)

I found a solution. I don't know why but seurat_obj$misc$active_wgcna hasn't been create properly, so i just had to create this variable:

seurat_obj@misc$active_wgcna <- "test"

and it work.

[smorabit]

Is anybody able to provide a reproducible example of this error on the latest version of hdWGCNA? I cannot reproduce it on my side.

[reJELIN]

So I did an singularity environment, I didn't have time to test it in order to see if the error is still there in this configuration. I can't give you any data because it is patient data.

As i said i think it come from a bad initialization of the misc$activate_wgcna variable in the seurat object. Perhaps in my case it is due to the fact that I used previously Seurat v4 for my annotation analysis and you're using Seurat v5 so may be the seurat object is kind working differently with your package.

Again this is working: seurat_obj@misc$active_wgcna <- "your_variable_name"