Help with subset seurat object by a column in metadata

Question

[Chris]

Hi all,

I try to subset seurat object by sample:

subset(x = combined_seurat_large, subset = sample == "1") Error in .subscript.2ary(x, i, j, drop = drop) : subscript out of bounds

I found other people asked this error on the internet but don't have a clear answer yet. Would you please have a suggestion? The error persists with seurat version 4.3 and 5.1. Thank you so much!

[gglim]

Seems that the bug still exists and they are working on it.

...and maybe you should try switch to Scanpy as @stefanonard85 said here: github issue

[Chris]

Thank you for the suggestion. Another way is to recreate the seurat object and use only the sample you want.

[bk11]

If sample is one of the column in meta.data, you can subset sample "1" using following commands:

Idents(combined_seurat_large) <- "sample" 
sample <- "1"
subset(skin, idents = sample, invert = FALSE)

[Chris]

Thank you for your reply! Unfortunately, I got the same error message.