hi, I have treatments A, B and C and controls a, b and c for 33603 genes. my adviser asked me to find 'Fold change difference in expression level of ''each gene'' at ''each time point '' when treatments compared to control condition'
then I subtracted raw counts or FPKM for treatment A and control a and so on. If I got her mean properly???? I presented the cuffdiff output but she told I should provide something else but I can't get her. could you get her please?