Suppose there is cohort with many samples to assay. In phase I of the project, subjects with a certain disease incidence and healthy controls were assayed. Now, in phase II of the project, we are going to assay samples with another disease and analyze them with healthy controls from phase I of the project. From past experience, we know that we have to assay healthy controls from phase I (whose bio samples are still available for assay) to avoid batch effects between phase I and phase II of the project. However, I don't know how much duplicate samples I should include and how the duplicates should be distributed.
My question is certainly related to experiment design, and perhaps there have been extensive discussions on this kind of design, but I don't know the exact term of this kind of experiment design such that I couldn't find anything relevant to my case in the literature. Can anyone point me to references related to this kind of experiment design?