I am trying to write a script in python to analyse my qPCR data, however I get confused with terminology how to report and plot results. I'd appreciate some advice on how to do this properly
What is the best way to report the results? In my lab they usually report mRNA expression of the Gene of Interest (GOI) relative to the reference gene, but the numbers you get seem quite irrelevant from my point of view; if you plot them, however, you clearly see the differences. I am also aware of the fold change, which seems more relevant if you just report the value, but when you plot them I think there's the problem that it's skewed to upregulated genes (which can go from one to infinity, whereas the downregulated ones can just be from 0 to 1).
To solve the latter, I have seen recommendations to plot log2 fold change, but that seems weird, because isn't that just the same value as ddCt?
If you do recommend reporting the fold change, what kind of error bars should I use when making the bar plot? Are the distributions still normal?
Thank you very much!