non balanced design in DESeq2

[libro.s]

Hi,
I apologize in advance if this question has been already asked but I`m wondering if DESeq2 can handle a non factorial design. Let`s say I have 2 factors A and B, A has 2 levels and B has 3. Each of the 2 levels of A is treated with each level of B, except 2 samples where only one level of B could be recovered. One option is obviously to exclude those 2 samples, but I was wondering if there is a way to include them in the analysis and increase the sample size.
Thank you in advance!

Silvia

[dpryan]

You can do incomplete factorial designs with DESeq (or edgeR or limma).