How to integrate-remove batch effects and assign cells

[francescopatane96]

Hi! From my kwnoledge, integrateLayers works on a low dim representation, so it does not modify counts or data. If I want to integrate and assign cells (many tools operate on raw counts) what is the best strategy for doing so? Thank you

[mhkowalski]

Do you mean tools that provide annotation predictions, like our Azimuth tool? I would recommend performing prediction separately for each "batch", rather than trying to used the corrected counts.

[francescopatane96]

Thank you for the reply and for the valuable suggestion. In doing so, does azimuth perform an integration step? How can i align my samples? I feel confused