Design with paired samples rna-ribo

[neusmf]

Hi!
Thanks for the package, it is very useful and clear!

I was wondering if it is possible to take into account that the rna and ribo samples are paired. I am asking this becuase I have three replicates and one replictae is a bit different than the others in both, RNA and RPF sequencing, so I think that providing the information that the RNA and RPF samples are paired will improve the results.

I tried with the multi-factor function but it says the matrix is not full rank. This is the conditions matrix for both datasets (rna and ribo):
treat samp
cont1 control 1
cont2 control 2
cont3 control 3
treat1 treatment 4
treat2 treatment 5
treat3 treatment 6

If I number the treatment from 1 to 3 then I have a matrix of full range but the results do not have sense, as the control and the treatment samples are not really paired.

I would like to know if my experimental design is possible.
Thanks for your help,
Neus