I have a question about the design of a DESeq2 experiment analysing RNA seq data. I have 3 factors to take into account: condition, patient and cell type. I have 2 conditions: normal and leukaemia. Within each condition I have multiple patients (please note this is an unpaired design and I do not have data from the same individual in both the normal and leukaemia condition). Within each patient there are 2 possible cell types: A and B. I am mostly interested in the overall condition effect, controlling for the differences across patients and cell types.
After reading the vignette, I tried creating a nested factor for the patient, giving the following:
As described in the vignette, I also removed the levels missing from an interaction of factors. I then tried using the following design: ~condition + condition:patient.nested + condition:cell type. However I still encounter the 'model matrix not full rank' error.
I'd appreciate any help on the design of this and advice on whether I have used the correct approach. Thank you!