Hi, I'd like to know what would be the best tool to analyze differentially expressed genes in an infection time course assay using 2 phenotypes.
I'm explaining, we did grow macrophages from 2 differents groups, healthy and sick animals (8 animals each phenotypes). Afterward, we did an infection time course (uninfected control, infection 1h, infection 4h, infection 8h, infection 12h and infection 24h).
Now I would like to visualize if the response from the cells of healthy animals differs from the one of sick animals. What would be the best way to do it? In all the case I want to keep the comparison of the infections time points with the uninfected controls, cause I already know that my controls are differents from animal to animal.
I used Deseq2 to compare each time points to my control, but I'd like to use a model where the phenotype is taken into consideration.