Re: Experimental design for multiple-batch study
Reply #1 –
If you have "paired samples" where you are not interested in the differences within the pairs it can reduce variance to put them in the same batch. For example if you have several persons you might consider having the same person in the same batch for all time course samples.
But as you say. Spread evenly conditions and randomize within the batch.
Use plenty of QC samples so that you afterwards can correct for potential intra- and inter-batch drifts.