Let's say that I have four groups of genes controlling the same function with opposing effects, two groups are stimulatory and the other 2 are inhibitory. I have RTPCR data for every gene in normal and disease state and I want to analyse the expected function change. What is the best way to analyse this? and what is the best way to graph it?

Can I use PCA for RTPCR results? so many questions but they are really important for my analysis

TIA