Hi, I am new to batch effect correction and apologize if this is a naive question.

My goal is to determine how similar my cell line is to the same cell line from an online database. I have the RNA-seq profiles for both samples, but they are obviously from two different batches, and any possible biological differences are confounded with batch.

A colleague of mine suggested that I can still batch effect correct to check similarity, by simply including other cell lines from the online database. So batch 1 would be my sample of cell line A, and batch 2 would include samples of cell line A, B, C, D, and E.

I used CombatSeq for this, and did not tell CombatSeq the identities of the cell lines. After batch effect correction, I see that indeed my sample of cell line A is now closer in the PC plot to the online database's sample of cell line A. Is this analysis valid?

Thanks!