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EDePasquale / DoubletDecon

A tool for removing doublets from single-cell RNA-seq data

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Improved_Seurat_Preprocessed() in DoubletDecon gives error

karthikavarmar opened this issue · comments

commented

I've a SeuratObject Leaf_frozen and I'm using this data into DoubletDecon's Improved_Seurat_Pre_Process() as shown below-

Leaf_processed <- Improved_Seurat_Pre_Process(Leaf_frozen, num_genes=50, write_files=FALSE)

which throws output and error -

Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Ensuring keys are in the proper structure
Ensuring feature names don't have underscores or pipes
Updating slots in RNA
Validating object structure for Assay5 ‘RNA’
Object representation is consistent with the most current Seurat version
Error in as.data.frame(seuratObject@assays[["RNA"]]@CountS) :
no slot of name "counts" for this object of class "Assay5"

This link shows detailed information on the said issue raised before if needed - satijalab/seurat#8210

@EDePasquale Please suggest a solution soon.

commented

Having this issue too. Changing seuratObject@assays[["RNA"]]@counts) to GetAssayData(seuratObject, assay = "RNA", layer = "counts") should solve the problem.