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smorabit / hdWGCNA

High dimensional weighted gene co-expression network analysis
https://smorabit.github.io/hdWGCNA/
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Got error message "GetAssayData doesn't work for multiple layers in v5 assay" #214

Closed shadowdeng1994 closed 3 months ago

shadowdeng1994 commented 3 months ago

I got the following message when I tried to run SetDatExpr on an integrated Seurat object. How can I solve it?

Warning message in SetDatExpr(tmp.hdWGCNA, group_name = "0", group.by = "seurat_clusters"): “assay not specified, trying to use assay SCT” Error in GetAssayData(): ! GetAssayData doesn't work for multiple layers in v5 assay. Traceback:

  1. SetDatExpr(tmp.hdWGCNA, group_name = "0", group.by = "seurat_clusters")
  2. as.data.frame(Seurat::GetAssayData(s_obj, assay = assay, slot = slot)[genes_use, . cells])
  3. Seurat::GetAssayData(s_obj, assay = assay, slot = slot)
  4. GetAssayData.Seurat(s_obj, assay = assay, slot = slot)
  5. GetAssayData(object = object[[assay]], layer = layer)
  6. GetAssayData.StdAssay(object = object[[assay]], layer = layer)
  7. abort("GetAssayData doesn't work for multiple layers in v5 assay.", . " You can run 'object <- JoinLayers(object = object, layers = layer)'.")
  8. signal_abort(cnd, .file)
rootze commented 3 months ago

@shadowdeng1994 This error is due to the Seurat V5 updates.

README

Note about Seurat v5: We plan to test the compatibility of hdWGCNA with Seurat version 5, but we have currently not updated hdWGCNA to work with Seurat v5. We strongly suggest using Seurat v4 at this time, or use v5 at your own risk.

smorabit commented 3 months ago

hdWGCNA does not work with Seurat v5 at this time. Actively working on an update for v5 support and it will be ready in a few weeks. Please continue to use Seurat v4 as suggested in the tutorial until we release an update for v5 support.