Error in .subset2(x, i, exact = exact) : subscript out of bounds

[Runzhi819]

Excuse me, I‘m tryign to use Convert_Assay to convert the V5 SeuratObject to V4 SeuratObject

# my code
scRNA = CreateSeuratObject(scRNA.counts ,min.cells = 3,project="os", min.features = 300)
install.packages("scCustomize")
library(scCustomize)
scRNA_V4 <- Convert_Assay(seurat_object = scRNA, convert_to = "V3")

sessionInfo() output

my result

> scRNA_V4 <- Convert_Assay(seurat_object = scRNA, convert_to = "V3")
Converting assay "RNA" from Assay5 to Assay.
Error in .subset2(x, i, exact = exact) : subscript out of bounds

What can I do to debug？

[samuel-marsh]

Hi @Runzhi819,

So the issue here is due to how Seurat operates and the as function. Basically, if an object does not have normalized and scaled data then the function cannot convert between assay types. Convert_Assay simply wraps this with some additional checks. So it's more meant to be used to convert already in process analyzed objects between formats.

I will add a check in next version to create a more informative error message for this situation.

In meantime though there is easy solution if you are creating an object from scratch. Simply run:

options(Seurat.object.assay.version = "v3")

Then create the object and it will be in V3/4 format. However, you will need to run:

options(Seurat.object.assay.version = "v5")

before creating your next V5 formatted object.

Best,
Sam