Flow cytometry on 29 healthy and 21 infected individuals. For healthy individuals, measured proportions of cells of 5 different types once. For infected individuals, measured proportions 3 times at different stages in the infection. Scientific question is to understand differences between healthy and infected individuals and temporal changes in the infected group in cell type proportions.
A repeated measures MANOVA is one possible approach to analyze the infected individuals. We would typically use SAS to fit models like these. It appears you can do a repeated measures MANOVA, but this may not allow an appropriate correlation structure for both healthy and infected individuals.
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