Entering edit mode
12 days ago
wykpenguin
•
0
I made a SCE object from a seurat object but it is acting strangely.
seurat_object
An object of class Seurat 85012 features across 6078 samples within 2
assays Active assay: RNA (55403 features, 0 variable features) 2
layers present: counts, data 1 other assay present: SCT
Converting it to SCE with inbuilt function in Seurat seemed to go fine:
sce_object <- as.SingleCellExperiment(seurat_object)
sce_object
class: SingleCellExperiment dim: 55403 6078 metadata(0):
assays(2): counts logcounts
rownames(55403): Xkr4 Gm37180 ... mt-Tt mt-Tp
rowData names(0):
colnames(6078): P10_AAAGGATCAGCTACCG-1
P10_AAAGTCCCAACTGAAA-1 ... P28_20RM_TTTGGAGTCTGCTTTA-1
P28_20RM_TTTGGTTAGCGACATG-1
colData names(21): orig.ident nCount_RNA ... SubclusterGroups Stage
reducedDimNames(0): mainExpName: RNA
altExpNames(1): SCT
length(rownames(sce_object))
55403
length(sce_object$Stage)
6078
However, when I check
length(rownames(sce_object$Stage))
0
Am I entering my metadata in the wrong slot in the SCE object?