Subset Seurat Object based on metadata

Question

[Bine]

Good afternoon,

I am trying to filter my Seurat object based on metadata with

Pancreas_Object<- subset(x = Pancreas_Object, subset = sample_type=='solid tumor')

However, I get the following error:

> RNA assay doesn't leave any cells, so it is removed Error in
> subset.Seurat(x = Pancreas_Object, subset = sample_type == "solid
> tumor") :    No cells left in the default assay, please change the
> default assay

I dont understand why it says "RNA assay doesnt leave any cells". I clearly have cells for this sample_type.

There is only one assay ("RNA") no integrated data or similar.

Thank you for any input!

[Anton]

Hi Bine,

Have you figured out how to solve your problem? I am facing the exact same issue.

Best regards,
Anton

[Ram]

P.S: Please do not add answers unless you're answering the top level question. Instead, use Add Comment or Add Reply as appropriate. I've moved your post to the right location this time, please be more careful in the future.

[bk11]

You can try this-

Idents(Pancreas_Object) <- "sample_type" 
cell_values <- c("solid tumor")
Pancreas_Object_subset <- subset(Pancreas_Object, idents = cell_values, invert = FALSE)

[Bine]

Thank you, but unfortunately I still get the same error:

> Idents(C1Q_Object) <- "sample_type" 
> cell_values <- c("solid tumor")
> Pancreas_Object_subset <- subset(C1Q_Object, idents = cell_values, invert = FALSE)
Error in subset.Seurat(C1Q_Object, idents = cell_values, invert = FALSE) : 
  No cells left in the default assay, please change the default assay

Answer 1

[aurelien.pelissier.38]

That's likely because the rownames in your seurat metadata do not match the colnames of your count matrix

you can compare them with

> colnames(GetAssayData(seurat_object, assay = "RNA", slot = "counts"))
> rownames([e-mail])

Best, Aurel