Hello, I am a novice and I am interested in comparing two kind of cells coming from different RNA sequencing experiments published. The design would be something like the following:

sample    cell    batch
1    type1    1
2    type1    1
3    type1    1
4    type1    2
5    type1    2
6    type2    3
7    type2    3
8    type2    3
9    type2    4
10   type2    4

Now, naturally I cannot model del batch effect with ~ batch + cell because the batch is nested in the condition "cell". But the question remains, what is the best way to compare type 1 and type 2 taking into consideration and mitigating possibile batch effects?

Thanks for your help. Best, Marco

The short answer is that you can't do that. There's no way to resolve the confounding.