I find the
reconstructed value after fastMNN is not readable.
For example, here is my interesting gene in replicate 1
and here is in replicate 2
As you can see, I can see the gene may express in specific some cells. And for people who is not familar with scRNA-seq, they can get the same information as me. And here is the vilion plot
But if I want to show the gene in merged UMAP after fastMNN using the reconstructed value, it seems for other people that this gene is expressing eveywhere while some cells express high and some cells express low count.
So I am wondering whether some one can give me some advices about it.