 # Dive into Diagnostics for DOE Model Discrepancies

Shari Kraber on Aug. 15, 2023

Note: If you are interested in learning more, and to see these graphs in action, check out this YouTube video “Dive into Diagnostics to Discover Data Discrepancies

The purpose of running a statistically designed experiment (DOE) is to take a strategically selected small sample of data from a larger system, and then extract a prediction equation that appropriately models the overall system. The statistical tool used to relate the independent factors to the dependent responses is analysis of variance (ANOVA). This article will lay out the key assumptions for ANOVA and how to verify them using graphical diagnostic plots.

The first assumption (and one that is often overlooked) is that the chosen model is correct. This means that the terms in the model explain the relationship between the factors and the response, and there are not too many terms (over-fitting), or too few terms (under-fitting). The adjusted R-squared and predicted R-squared values specify the amount of variation in the data that is explained by the model, and the amount of variation in predictions that is explained by the model, respectively. A lack of fit test (assuming replicates have been run) is used to assess model fit over the design space. These statistics are important but are outside the scope of this article.

The next assumptions are focused on the residuals—the difference between an actual observed value and its predicted value from the model. If the model is correct (first assumption), then the residuals should have no “signal” or information left in them. They should look like a sample of random variables and behave as such. If the assumptions are violated, then all conclusions that come from the ANOVA table, such as p-values, and calculations like R-squared values, are wrong. The assumptions for validity of the ANOVA are that the residuals:

• Are (nearly) independent,
• Have a mean = 0,
• Have a constant variance,
• Follow a well-behaved distribution (approximately normal).

Independence: since the residuals are generated based on a model (the difference between actual and predicted values) they are never completely independent. But if the DOE runs are performed in a randomized order, this reduces correlations from run to run, and independence can be nearly achieved. Restrictions on the randomization of the runs degrade the statistical validity of the ANOVA. Use a “residuals versus run order” plot to assess independence.

Mean of zero: due to the method of calculating the residuals for the ANOVA in DOE, this is given mathematically and does not have to be proven.

Constant variance: the response values will range from smaller to larger. As the response values increase, the residuals should continue to exhibit the same variance. If the variation in the residuals increases as the response increases, then this is non-constant variance. It means that you are not able to predict larger response values as precisely as smaller response values. Use a “residuals versus predicted value” graph to check for non-constant variance or other patterns.

Well-behaved (nearly normal) distribution: the residuals should be approximately normally distributed, which you can check on a normal probability plot.

A frequent misconception by researchers is to believe that the raw response data needs to be normally distributed to use ANOVA. This is wrong. The normality assumption is on the residuals, not the raw data. A response transformation such as a log may be used on non-normal data to help the residuals meet the ANOVA assumptions.

Repeating a statement from above, if the assumptions are violated, then all conclusions that come from the ANOVA table, such as p-values, and calculations like R-squared values, are wrong, at least to some degree. Small deviations from the desired assumptions are likely to have small effects on the final predictions of the model, while large ones may have very detrimental effects. Every DOE needs to be verified with confirmation runs on the actual process to demonstrate that the results are reproducible.