Since we have a rather complicated experimental design we would like to get
We have 70 samples from 40 patients. Each sample was collected from a different time interval (ID and RE) based on the disease stage. For 10 patients there is only 1 sample available. We would like to find the differentially expressed genes between subtype1 and subtype2, in which the patients are divided.
For example, this is how our design look like,
Our concern is that are we boosting certain genes by having two samples from the same patients, how could we account for that using a multifactorial design? Should we account for additive effect ( ~ condition+patient ) or also interaction (~ condition*patient )?
Thanks for all opinion and suggestions