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smorabit / hdWGCNA

High dimensional weighted gene co-expression network analysis
https://smorabit.github.io/hdWGCNA/
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Error in the ModulePreservation step #208

Closed loganminhdang closed 2 months ago

loganminhdang commented 4 months ago

Thank you so much for this great package; I have been a fan of WGCNA for a long time. While running the ModulePreservation step for my cross-modality data (single-cell RNA-seq and single-cell ATAC-seq), I received the following error: Error in WGCNA::modulePreservation(multiExpr, ref_modules, referenceNetworks = 1, : Color vector for set 1 does not have the correct number of entries.

I cannot deduce what the error might be related to and have attempted numerous strategies to troubleshoot to no avail. Would this be related to a disparity in the number of modules between the two modalities of data?

The code I used was: seurat_atac <- ModulePreservation( seurat_atac, seurat_ref = seurat_ref, wgcna_name = "Epi_multiome", wgcna_name_ref = "epi_standard", name="Epi-ATAC", verbose=3 )

R session info R version 4.3.2 (2023-10-31) 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_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/London tzcode source: system (glibc)

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

other attached packages: [1] ggforestplot_0.1.0 igraph_1.6.0 WGCNA_1.72-5 fastcluster_1.2.6
[5] dynamicTreeCut_1.63-1 patchwork_1.1.3 cowplot_1.1.2 lubridate_1.9.3
[9] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
[13] readr_2.1.5 tidyr_1.3.0 tibble_3.2.1 tidyverse_2.0.0
[17] EnsDb.Mmusculus.v79_2.99.0 ensembldb_2.26.0 AnnotationFilter_1.26.0 GenomicFeatures_1.54.1
[21] AnnotationDbi_1.64.1 Biobase_2.62.0 hdWGCNA_0.2.26 ggrepel_0.9.4
[25] ggplot2_3.4.4 harmony_1.2.0 Rcpp_1.0.11 SeuratObject_5.0.1
[29] Seurat_4.0.3 Signac_1.12.9004 GenomicRanges_1.54.1 GenomeInfoDb_1.38.5
[33] IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1

smorabit commented 3 months ago

Hi,

I have not personally come across this error but I can probably help if you can provide some more details. Can you explain a bit more about what you did before you ran ModulePreservation? Did you make sure to run ProjectModules and SetDatExpr in the query dataset like we showed in the tutorial?

I am confused when you say:

Would this be related to a disparity in the number of modules between the two modalities of data?

Module preservation is checking whether the co-expression modules that were identified in the reference dataset are preserved in the query dataset, it is not about comparing two different sets of modules to one another.

smorabit commented 2 months ago

Closing this issue for now due to inactivity.