I have a question that I can't seem to figure out. I have protein data for 2 different treatments (3 samples each) and only 1 control sample. I want to run some statistics to find differences between the 2 treatment conditions but using the control because it is important for this experiment. Someone suggested to me to calculate FC for each treatment sample using the one control sample and then converting these ratios to z-scores. I have converted them to z-scores now (so for each protein I have 3 z-scores in treatment 1 and 3 z-scores in treatment 2. Is this way acceptable? Also I'm wondering how to get 1 p-value out of these for each protein?
Thanks a lot!