Thank you for providing such a useful tool. When using Harmony for batch correction, I noticed that tumor cells in different samples show distinct separation, while normal cells cluster by cell type. Even when I apply Harmony separately to tumor cells, they still do not aggregate.
I'm uncertain whether this indicates significant differences in chromatin accessibility among tumor cells across samples or if it's due to issues with my processing methods.
In this situation, do you have any suggestions?
Thank you for providing such a useful tool. When using Harmony for batch correction, I noticed that tumor cells in different samples show distinct separation, while normal cells cluster by cell type. Even when I apply Harmony separately to tumor cells, they still do not aggregate. I'm uncertain whether this indicates significant differences in chromatin accessibility among tumor cells across samples or if it's due to issues with my processing methods. In this situation, do you have any suggestions?