Starting from a Seurat object

[zznx]

Hi, In tutorial

data.input <- seurat_object[["RNA"]]@data # normalized data matrix
# For Seurat version >= “5.0.0”, get the normalized data via `seurat_object[["RNA"]]$data`
labels <- Idents(seurat_object)
meta <- data.frame(labels = labels, row.names = names(labels)) # create a dataframe of the cell labels

I'm curious if the following result is better or worse?

data.input <- seurat_object[["SCT"]]@data # normalized data matrix
# For Seurat version >= “5.0.0”, get the normalized data via `seurat_object[["SCT"]]$data`
labels <- Idents(seurat_object)
meta <- data.frame(labels = labels, row.names = names(labels)) # create a dataframe of the cell labels

[lalalay818]

Do you have an answer now? I have the same question.