I have a normalized and batch effect removed microarray data. I have 5 groups of samples namely S1 to S5. I have to find differentially expressed genes in 3 conditions below:
1) one group vs remaining groups (for example S2 VS S1,S3,S4,S5)
2) differentially expressed genes across all 5 groups
3) all comparisons between 2 groups.
I just wanted to know how should I define my questions in model.matrix() and makeContrasts() functions to analyze my data.