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smorabit / hdWGCNA

High dimensional weighted gene co-expression network analysis
https://smorabit.github.io/hdWGCNA/
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How to fix "Error in getClassDef(x@superClass, package = packageSlot(x))@virtual : no applicable method for `@` applied to an object of class "NULL" " #172

Closed danL9018 closed 5 months ago

danL9018 commented 6 months ago

when Construct metacells Run the code and showed the Error in getClassDef(x@superClass, package = packageSlot(x))@virtual : no applicable method for @ applied to an object of class "NULL"

Steps to reproduce the code I used "WratVF1 <- MetacellsByGroups(WratVF1, group.by =c("celltype"), reduction = "pca", k = 25, max_shared = 10, min_cells = 30, ident.group = "celltype", cells.use = NULL ) " to generate the error. The code to setup for WGCNA "WratVF1 <- SetupForWGCNA(WratVF1, gene_select = "fraction", fraction = 0.05, wgcna_name = "ratVF hdWGCNA", group.by = "celltype")". The data set I used is a scRNA-seq data set of SD rat larynx.

p <- DimPlot(WratVF1 , group.by='celltype', label=TRUE) +
  umap_theme() + ggtitle('rat VF') + NoLegend()

p

WratVF1  <- SetupForWGCNA(WratVF1, gene_select = "fraction", fraction = 0.05, wgcna_name = "ratVF hdWGCNA", group.by = "celltype")
WratVF1 <- MetacellsByGroups(WratVF1, group.by =c("celltype"), reduction = "pca", k = 25, max_shared = 10, min_cells = 30, ident.group = "celltype", cells.use = NULL )

R session info R version 4.3.2 (2023-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22631)

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smorabit commented 6 months ago

Hi,

Thank you for using hdWGCNA and for sharing your issue. I have not personally come across this issue before. Are you able to reproduce this error on the tutorial dataset or does this only happen on your dataset?

Ldec12 commented 6 months ago

Hi I met the same error as well, I changed the version of the Matrix package to 1.6.1.1, and re-installed SeuratObject. it works well now.

danL9018 commented 6 months ago

Thanks a lot! I have renewed the version of Matrix, Seurat and SeuratObject.

在 2023-11-16 11:55:52，"Ldec12" @.***> 写道：

Hi I met the same error as well, I changed the version of the Matrix package to 1.6.1.1, and re-installed SeuratObject. it works well now.

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