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smorabit / hdWGCNA

High dimensional weighted gene co-expression network analysis
https://smorabit.github.io/hdWGCNA/
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SetDataExpr Error #178

Closed vasikara17 closed 5 months ago

vasikara17 commented 5 months ago

Hello, I have a question regarding SetDataExpr function. I run : ###Set up the expression matrix seurat_obj <- SetDatExpr( seurat_obj, group_name = "Adipocytes_2", # the name of the group of interest in the group.by column group.by='seurat_clusters', # the metadata column containing the cell type info. This same column should have also been used in MetacellsByGroups assay = 'RNA', # using RNA assay slot = 'data' # using normalized data )

Error in GetAssayData(): ! GetAssayData doesn't work for multiple layers in v5 assay. Run rlang::last_trace() to see where the error occurred.

Does this have to do with the Seurat version I am using? Best wishes, Vasiliki

smorabit commented 5 months ago

Yes this is a Seurat v5 related issue. We have not yet updated hdWGCNA to work with Seurat 5 so please use Seurat 4 for now.