annotation before integration

Question

[Andy]

Good evening everyone,

I have a question. My single cell dataset is huge, and I did not integrate it well. My professor suggested that I should annotate the dataset first, then proceed with the integration. By doing this and still applying the same integration method, it indeed improves the integration output. I am wondering, what is the reason for this?

Thanks

Andy

[Ming Tommy Tang]

what do you mean by annotating the dataset first? Do you mean by annotating the clusters? and how that affects how you integrate the data?