Adata obs not consistent after merge


I’m working with two large single cell datasets of similar makeup. One of my obs categories for each dataset is ‘sex’, either male or female.

In either dataset separately, I’m seeing gene A more highly expressed in females than in males in a certain cell type. However, after merging my data I see the opposite - gene A is more highly expressed in males and is almost not present in females at all. I’ve copied the code I’m using below to concatenate - am I passing in the wrong argument somewhere?

test3 = run1.concatenate(run2, batch_key = ‘batch’, batch_categories = [‘first’, ‘second’], join = ‘outer’, index_unique = None)