bulk RNA-seq: how to remove batch effect between multiple batches and labels?

Question

[kiraqueen]

Hi. I have 3 batches of RNA-seq data, A, B and C (having obvious differences in PCA plot) A and B with mixed tags i.e. 1, 0 (and supposed to have different expression pattern) C with only 0 label.

so how can i correct the batch effect but keep the real biological differences? would using combat twice for each label group's samples work?

I would be grateful if someone could give me any suggestions!