For a fractional factorial design, some of the main effects are going to be confounded (typically referred to as “aliased” within the factorial literature) with higher-order interactions, and thus the subset of experimental conditions needs to be carefully selected so that the main effects are only aliased with higher-order interactions that are judged to be less likely to be significant (e.g., 3-way or 4 way-interactions) or of less theoretical interest.
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