I've got a paired experiment with a setup like below.
The x's indicate a sample present. Each sample is a primary cell culture preparation from the same donor, and treated with one of three agonists and a vehicle control. I want to contrast each agonist independently against the control (Agonist 1 vs Control, Agonist 2 vs Control, Agonist 3 vs Control), but wondered how to address the missing data.
Reading the response on DESeq2 paired design with missing samples and multiple conditions, it seems like I have a similar situation, however, I want to confirm. My main interest is estimating the condition effects while controllign for the sample effect.
As far as I can tell, it seems like I could use the design ~Sample + condition then contrast the results object. Would this be recommended or would it be better to either subset the data or use limma-voom?