Converting SingleCellExperiment objects into Seurat objects #6692
Closed
Description
Hello,
I am having trouble converting SingleCellExperiment objects from the scRNAseq bioconductor collection using as.Seurat
. Here's a reproducible example:
BiocManager::install('scRNAseq')
library(scRNAseq)
sce <- ZilionisLungData('mouse')
seurat <- as.Seurat(sce, counts = "counts", data=NULL)
Error in embeddings[i, j, drop = drop, ...] : subscript out of bounds
Several other datasets in the collection give similar errors. Any idea what's going on here? can I e.g. ask as.Seurat
to only convert counts and metadata?
Thanks in advance,
-massimo
Activity
alikhuseynov commentedon Nov 18, 2022
Hi,
..same issue as well.
it only works when removing embeddings (maybe something is wrong with them in that
sce
object)timoast commentedon Dec 7, 2022
The problem with this dataset is many of the cell names are duplicated:
This is unusual, and we require that within a Seurat object a cell name is unique to one cell. The issue here is that we are automatically renaming cells with conflicting names, but that renaming is not being performed on the dimension reduction object
Fix sce object conversion; #6692