I am trying to decide on the best design for my EdgeR differential-expression analysis. I have RNA-seq data from four patients - matched blood and liver for three of the patients and only liver from one of the patients (as below).
Donor Tissue 1 Blood 1 Liver 2 Blood 2 Liver 3 Blood 3 Liver 4 Liver
The two options I am considering for the design formula are:
- ~ Tissue
- ~ Donor + Tissue
Is it possible to use the second approach when one of the donors only has a liver sample? What is the best approach to get around this issue?
Many thanks for the advice.