I recently attempted an experimental set-up according to a fractional factorial design. At first, the idea was that I'd investigate 5 factors on two levels and I designed the experiment in accordance with a 2^5-2 design to keep the experiments limited.
However, along the way I excluded one factor but forgot to change my plan, I should have used a 2^4-1 plan but instead hang on to the old 2^5-2 plan - changing only 4 factors.
* Now, realizing that my data is not orthogonal when analyzed as a 2^4-1, should I analyse it as was it a 2^5-2 instead?
* What happens if my design isn't orthogonal?
(Factors A, B and C were according to yates normal order while the fourth factor is confounded with AB instead of ABC.)
Happy for some input on this, I seldom perform these kinds of tests...