Error when converting SCE object to Seurat despite counts and logcounts present in assays

[sagrikachugh]

I am using Seurat v5.0.2 , SeuratObject v5.0.1 and SingleCellExperiment v1.22.0 trying to convert a SCE object to Seurat using the following code

so <- as.Seurat(sce, counts = "counts", data = "logcounts")

This results in error:

Error: No data in provided assay - logcounts

Here is how my SCE looks like:

sce
class: SingleCellExperiment 
dim: 28421 111867 
metadata(1): Samples
assays(2): counts logcounts
rownames(28421): Xkr4 Gm1992 ... CAAA01147332.1 AC149090.1
rowData names(4): ID Symbol Type CHR
colnames(111867): 1_AAACCCACAAGTGACG-1 1_AAACCCACACTCACTC-1
  ... 15_TTTGTTGGTTAGTCGT-1 15_TTTGTTGGTTTGGGAG-1
colData names(29): Sample Barcode ... cluster cluster_colours
reducedDimNames(2): PCA UMAP
mainExpName: RNA

[Gesmira]

Can you share a small example file where this is occurring?

[sagrikachugh]

@Gesmira Thanks for looking into this.
Here's a reproducible example using the scater package

Creating a sce object first

test_sce <- scater::mockSCE()

test_sce
class: SingleCellExperiment 
dim: 2000 200 
metadata(0):
assays(1): counts
rownames(2000): Gene_0001 Gene_0002 ... Gene_1999 Gene_2000
rowData names(0):
colnames(200): Cell_001 Cell_002 ... Cell_199 Cell_200
colData names(3): Mutation_Status Cell_Cycle Treatment
reducedDimNames(0):
mainExpName: NULL
altExpNames(1): Spikes

Now, we add logcounts to the test_sce object as as.Seurat function needs both "counts" and "logcounts" in the assay slot

test_sce <- scater::logNormCounts(test_sce)

Now we have "logcounts" in our assays as shown below

test_sce
class: SingleCellExperiment 
dim: 2000 200 
metadata(0):
assays(2): counts logcounts
rownames(2000): Gene_0001 Gene_0002 ... Gene_1999 Gene_2000
rowData names(0):
colnames(200): Cell_001 Cell_002 ... Cell_199 Cell_200
colData names(4): Mutation_Status Cell_Cycle Treatment sizeFactor
reducedDimNames(0):
mainExpName: NULL
altExpNames(1): Spikes

Converting test_sce to seurat object

test_so <- as.Seurat(test_sce, counts = "counts", data = "logcounts")

This results in error -

Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')
Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')
Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')
Error: No data in provided assay - logcounts

[sagrikachugh]

@Gesmira Could you please have a look at the above example with mockSCE. It seems like a bug now.