Hello! I want to look at the differentially expressed genes between two groups (Healthy vs Infected) in single-cell data. However, I want to control for days post symptoms. How would I go about doing that? In bulk RNAseq I would usually set the design as ~group, group:time, however using MAST using this vignette (satijalab.org/seurat/v3.0/de_vignette.html) I don't see that option.
Would it be okay for me to set Healthy as day 7 and run this analysis - regressing time out?
Example data structure:
Pt3: Infected, 3 days post symptoms
Pt4: Infected, 7 days post symptoms
Pt5: Infection, 0 days post symptoms