ATACseq batch effect coupled with biological effect

Question

[pt.taklifi]

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?

[boaty]

Make a PCA plot with different color to inspect the effect batch, you will then learn if the batch is removable or confounded with biological factor.

[pt.taklifi]

can you please explain more ? because the two datasets are from biologically different cell types ( the first is from TCGA and the second is from healthy PBMCs) how could PCA separate cell type factor and batch effect ? Thank you

[boaty]

HI, PCA will not do the removal thing, it just give you the insight of your data, is it feasible or not? if in PCA plot, your data separate for cell type at PC1 and batch is separated at PC2 then you know you can do the removal