ATACseq batch effect coupled with biological effect

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I am currently working with ATACseq count matrix from two different datasets one contains data from let's say cell type A,B,C and the other dataset is from cell type D & E.
I am trying to do a binary classification ( fro example A vs. others ) . I think I need to do a batch effect removal step prior to this step , however since biological effect and batch effect are coupled here ,I'm not sure how to do it.
I was wondering if I should do a batch effect removal in this situation and if so how to implement it ?


ATACseq


batch_effect

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