I am trying to convert my single cell Seurat object to single cell experiment object. When I set the DefaultAssay to "RNA" the sce object does not retain HVGs and when it is set to "integrated" it does not retain count slot. I was wondering how I can retain all of the assays in sce object. Or if I apply the
getTopHVGs(als, n=1000) on sce object does it return the same HVGs?
Any comment would be appreciated.