I am performing a differential expression analysis between treated and untreated cell lines using DESeq2. The samples were sequenced in two different batches, however, there is a perfect confounding of the conditions and the batches. All controlled samples are in one batch and all treated samples are in the second one. The perfect confounding does not allow to remove batches or even account for them in the formula. I was wondering is it still valid to compare all treated conditions to the control and then compare the regulation of different genes in response to treatment? For example, I would like to check if AKT1 is upregulated in one treatment when compared to control and downregulated in another one when compared to control.