I am using REST2009 to look at expression changes of my target gene over time with 3 biological replicates for each time point. I am planning to analyze the data by comparing all time points individually (i.e. treated sample) to one common time point A (i.e control sample) to determine relative expression, i.e time point B relative to time point A, time point C relative to time point A, and so on.

I want to include time point A itself in this time series, but my question is, how do I analyze time point A itself (i.e. relative expression would be 1) so I get its SE? Do I enter the same Cq for both treatment and control? (see attached Excel sheet, e.g. reference gene for both control and treatment 17.52, 17.47, 17.40)

Or do I use the individual Cq for the treatment group and just use their average for the control? (see attached Excel sheet, e.g reference gene for treatment 17.52, 17.47, 17.40 and for control 17.464)