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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 #56

Open karthikavarmar opened 8 months ago

karthikavarmar commented 8 months ago

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 - https://github.com/satijalab/seurat/issues/8210

@EDePasquale Please suggest a solution soon.

qslin commented 4 months ago

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