I want to evaluate the level of gene expression by real-time PCR. I have five controls that are "clinically" the same. I calculated the "fold change" of the target gene regarding each control.
What if the result of "fold change" for my target gene is different for each control? I mean it is up regulated according to three of them and down-regulated according to the rest two.
Is the intervention biased? Or should I consider the average?