I'm using a design of experiments method, especially the Box-Behnken matrix. Now comes the time to plot some figures to see the effects of the three constants and I started to do it like in this paper:

http://www.sciencedirect.com/science/article/pii/S016816050700640X

The thing is that when studying 2 of the 3 constants, there are two results for the same point given the constitution of the matrix. Matlab automatically does an average of those two values but I wonder if it's really pertinent as the third value has an effect on the response. So is this method using the average still relevant to analyze the effects?

Can you suggest another method which could be better?

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