Scaling after conversion from anndata to seurat object

[pmarzano97]

Hello world!
I have a question related to the conversion from an anndata object (generated by Scanpy Python pakage) to a Seurat Object (seurat version 4.3.0).

In the workflow that I normally apply, when I create the anndata object I do not scale the counts stored in .X layer, I only run the following functions to normalize the counts:

• sc.pp.normalize_total(adata, target_sum = 1e4)
• sc.pp.log1p(adata)

I do not scale the counts since when I check the expression of markers via DotPlots/MatrixPlots/..., I use the option in the function standar_scale = 'var', so that the marker gene expression is scaled.

And here comes my question. When I convert the anndata object to a Seurat one, in the seuratobject the scale layer (seuratobject[["RNA"]]@scale.data) is empty. This means that I should scale the expression with the function ScaleData(seuratobject)?
The normalization is not necessary since the counts that I'm importing into the seuratobject are already normalized, but since in Seurat there is not the option to scale the expression within the DotPlot/... function, should I scale right after the conversion?

Thanks for the help!
Paolo