Hello,

I would like to summon Michael Love here and anyone else that can contribute. I was doing some research on DESeq2 and reading the following topic of the tutorial: Group-specific condition effects, individuals nested within groups, I was wondering if I can use this strategy to join different datasets, then each dataset will be treated as a group, each group will have their distinct individuals, and each individual will have two conditions (in common among all datasets). Does the design described account for the probable batch effect?

Thank you in advance.

Yes, this sounds reasonable and will estimate a fixed batch/dataset effect and help you estimate a fixed condition effect. If you wanted to get more complicated, you could attempt to estimate a random effect of condition, but this isn't supported within DESeq2. For what it's worth, I know there are some methods for RNA-seq that account for sample non-independence with random effects but I don't know of methods where the random effects are not nuisance parameters, but parameters of interest.