Scaling after mnn_correct

For some reason, after I do the mnn_correct, and then:

sc.pp.neighbors(bdata), color = ‘Batch’)

it will un-batch correct the data for some reason. I figured out that I shouldn’t scale it, and will leave it batch corrected … any idea why this occurs?

I don’t think this is correct, I think one should:, svd_solver = ‘arpack’, use_highly_variable = False), components = [‘1,2’,‘3,4’,‘5,6’,‘7,8’], ncols = 2,
color = ‘Condition’, save = “Corrected_pca_condition.pdf”), save = ‘_elbow.pdf’)

directly after receiving object fromm mnn_correct, as in :