Hello,
I'm working with a SCE object and trying to scale data to create my clusters. I am able to normalize the data to create the assay seuratNormData
but when I try to do the same with scaled data it shows the following output that seuratScaledData is saving under AltExp. However then when I try to find this data in my object afterwards it doesn't exist in AltExp
or under Assays
. No errors are popping up but it seems like it just doesn't actually apply the code to the object?
runSeuratScaleData(inSCE = sce, useAssay = "seuratNormData", scaledAssayName = "seuratScaledData")
Centering and scaling data matrix
|=====================================================================================================================| 100%
class: SingleCellExperiment
dim: 36601 243692
metadata(4): sctk assayType findMarker seurat
assays(3): counts decontXcounts seuratNormData
rownames(36601): MIR1302-2HG FAM138A ... AC007325.4 AC007325.2
rowData names(14): feature_ID feature_name ... var.features.rank hvf
colnames(243692): k1049_AAACCTGAGCCTTGAT-1 k1049_AAACCTGAGGCATGGT-1 ... sli202_TTTGTCAGTTGTGGAG-1
sli202_TTTGTCATCCTTGACC-1
colData names(25): cell_barcode column_name ... scds_hybrid_call cellSubtype
reducedDimNames(43): PCA UMAP ... seuratUMAP doubletFinder_UMAP
mainExpName: NULL
altExpNames(1): seuratScaledData
altExpNames(sce)
character(0)