Alternate DESeq2 designs to model donor variance
I have a set of RNASeq data; 3 treated replicates, 3 control replicates, from each of 4 donors. I observe in the PCA plot that my Treatment corresponds to PC3; PC1 and PC2 correspond to the donors. Usually, when running DESeq2 on this data, I'd use a formula of ~ Donor + Treatment, but someone suggested that instead of using Donor in the design, I could use ~ PC1 + PC2 + Treatment
Would this be valid? Would it be better than using Donor? Or just different?
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~ Donor + Treatmentand~ PC1 + PC2 + Treatmentproduce similar results? It would depend on how much variation is captured by PC1 and PC2, of course.Top genes were comparable. I think adjusted p values were better with PC1 and PC2 than using Donor.