Correct for batch effect in miRNA sequencing using reference sample

Question

[ricmelof]

Hi,

I have two sequencing experiments that I want to correlate. I don't have the same conditions in both experiments, only one condition is repeated across them, therefore I believe DEseq2 will not be able to correct for batch effect. Is this correct?

I do, however, have two samples repeated in both experiments. How can I use the expression of those samples to correct for batch effect?

Thank you