Kristof A Torkenczy

Hi, is any of your scale.data slots empty in one of your objects (either in the SCT or the RNA assay)?

Hi, you should provide a graph name in your object. E.g.: "RNA_snn" from obj.merge@graphs$RNA_snn.

Hi, could you post the code you are running and info on the two objects?

Different embedding seed perhaps? If you have the same uwot, Seurat or umap-learn then that is the only thing I can think of.

From what I am reading you want to get cell type specific signal and remove the signal that is common across treatments in multiple cell types. I would do your...