Maybe it is a simple question, but any help is appreciated.
I have a microarray dataset of 5 treatments/5 controls(in duplicate). The only experimental value for the treatment is, it has a score 2 for the disease whereas controls have score 0. I have used 5 treatments vs. 8K genes to cluster the genes. I would like to find out which cluster of genes are most correlated with the phenotype. Is there a way to do it?
Edit: The experiment is: rats are treated with 5 chemicals(duplicates) and they have corresponding controls without chemical treatment. These chemicals produce liver inflammation. The phenotype is measured as histopathology scores (discrete values) between 0 to 3. All treatments has a score of 2. After clustering I would like to select clusters that are most relevant to phenotype.