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

