We have performed a RNAseq experiment to understand the differential gene expression upon repression of a gene. We have generated a strain in which the gene of interest is placed under doxycycline (DOX) repressible promoter (genotype: tet90). When the DOX is added to medium, gene gets repressed. DOX also has its own effect on the overall gene expression and hence we also have the RNAseq data for WT strain treated with DOX. WT strain grown on YPD medium is used as control. Please refer below for the complete design matrix for details:
We would like to see the differential expression for gene repression condition vs normal condition (tet90_Dox vs tet90_YPD). However, we would also like to control for the DOX effect in this comparison. I think that this situation is similar to one of the Michael's reply in recent post on comparison (B-control_B) - (A-control_A) C: help DESeq2 model design. I have tried exploring other similar posts on forums but still could not come up with a design formula. What can be the appropriate design formula to address this problem in DESeq2?