I have the following experimental design (n=9). Trying to compare the two cell types.

Celltype 1 from individuals A, B, and C

Celltype 2 from individuals A, B, D, E, F, and G

Is there any way to include in the design the fact that 2/3 cell type 1 samples have a corresponding paired sample in cell type 2?

Right now I have just been running design=~Celltype. But if the design could include Individual in some way, I think that would improve the power a lot.

Willing to remove the sample from individual C if needed.

I tried running without and without individual C, using design=~Celltype + Celltype:Individual and removing all-zero columns from the model matrix. But this produces the following error:

Error in checkForExperimentalReplicates(object, modelMatrix) :

same number of samples and coefficients to fit with supplied model matrix

So maybe this just doesn't make sense to do?