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Subset Seurat Object based on metadata

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 don't understand why it says "RNA assay doesn't 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!

seurat
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updated by Ram Ram • written by Nona • Nona

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)
• 0 views • link
written by bk11 • bk11

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
• 0 views • link
updated by Ram Ram • written by Nona • Nona

Hi Bine,

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

Best regards,
Anton

• 0 views • link
updated by Ram Ram • written by Anton • Anton

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.

• 0 views • link
written by Ram Ram

2 answers

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(seurat_object@meta.data)

Best,
Aurel

• 0 views • link
updated by Ram Ram • written by aurelien.pelissier.38 • aurelien.pelissier.38

Hi all,

I recently also encountered the same error: "RNA assay doesn't leave any cells, so it is removed.." when I am doing the subset function in Seurat package:

gse262072_basal <- subset(gse262072, subset = GroupID=="Basal")

Here is my solution: check the cell names between the assay data and the metadata

rownames(gse262072@meta.data)[1:5] [1]
"CD_02_s_CARTQ_AAACCCACATGGCCAC-1" "CD_02_s_CARTQ_AAACGAACAGCTATAC-1"
"CD_02_s_CARTQ_AAACGAACAGTTAGAA-1" [4]
"CD_02_s_CARTQ_AAACGAATCGCTTGCT-1" "CD_02_s_CARTQ_AAAGAACAGAGGGTGG-1"

gse262072@assays$RNA@data@Dimnames[[2]][1:5] [1]
"CARTQ_AAACCCACATGGCCAC-1" "CARTQ_AAACGAACAGCTATAC-1"
"CARTQ_AAACGAACAGTTAGAA-1" "CARTQ_AAACGAATCGCTTGCT-1" [5]
"CARTQ_AAAGAACAGAGGGTGG-1"

gse262072@assays$RNA@counts@Dimnames[[2]][1:5] [1]
"CD_02_s_CARTQ_AAACCCACATGGCCAC-1" "CD_02_s_CARTQ_AAACGAACAGCTATAC-1"
"CD_02_s_CARTQ_AAACGAACAGTTAGAA-1" [4]
"CD_02_s_CARTQ_AAACGAATCGCTTGCT-1" "CD_02_s_CARTQ_AAAGAACAGAGGGTGG-1"

Here, you can see the cell name in assay data was inconsistent with meta.data and assay counts. So, just simply run:

gse262072@assays$RNA@data@Dimnames[[2]] <-  gse262072@assays$RNA@counts@Dimnames[[2]]

Then, it works at my side.

Hope this could help you.

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updated by Ram Ram • written by JackShao • JackShao

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