I am working on finalizing some of my data for a manuscript, and I have recently started plotting my RT-qPCR data as the delta delta-CT, or the fold change compared to an untreated control. Historically, everyone in my lab has plotted qPCR data as the delta-CT, representing the difference in CT values for the genes of interest and the housekeeping gene (we use 18s). For these experiments, our "treated" animals have been prenatally exposed to alcohol and exposed to a stressor. The "untreated" animals in the control group (the group to which I'm comparing every other group to get the delta delta-CT) were not prenatally exposed to alcohol, and were not exposed to a stressor. To maintain a balanced experimental design, we also have animals that were prenatally exposed to alcohol but not stressed, as well as animals that were not prenatally exposed to alcohol and then exposed to the stressor. What advantages might there be to plotting the delta-CT instead of the delta delta-CT? The only reason I can think of why someone would not want to plot the delta delta-CT is if the "untreated" group does not represent a true control.