# 1.2 - The Basic Principles of DOE

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The first three here are perhaps the most important...

Randomization - this is an essential component of any experiment that is going to have validity. If you are doing a comparative experiment where you have two treatments, a treatment and a control for instance, you need to include in your experimental process the assignment of those treatments by some random process. An experiment includes experimental units. You need to have a deliberate process to eliminate potential biases from the conclusions, and random assignment is a critical step.

Replication - is some in sense the heart of all of statistics. To make this point... Remember what the standard error of the mean is? It is the square root of the estimate of the variance of the sample mean, i.e., $\sqrt{\frac{s^2}{n}}$. The width of the confidence interval is determined by this statistic. Our estimates of the mean become less variable as the sample size increases.

Replication is the basic issue behind every method we will use in order to get a handle on how precise our estimates are at the end. We always want to estimate or control the uncertainty in our results. We achieve this estimate through replication. Another way we can achieve short confidence intervals is by reducing the error variance itself. However, when that isn't possible, we can reduce the error in our estimate of the mean by increasing n.

Another way is to reduce the size or the length of the confidence interval is to reduce the error variance - which brings us to blocking.

Blocking - is a technique to include other factors in our experiment which contribute to undesirable variation. Much of the focus in this class will be to creatively use various blocking techniques to control sources of variation that will reduce error variance. For example, in human studies, the gender of the subjects is often important factor.  Age is another factor affecting the response.  Age and gender are often considered nuisance factors which contribute to variability and make it difficult to assess systematic effects of a treatment.  By using these as blocking factors, you can avoid biases that might occur due to differences between the allocation of subjects to the treatments, and as a way of accounting for some noise in the experiment. We want the unknown error variance at the end of the experiment to be as small as possible. Our goal is usually to find out something about a treatment factor (or a factor of primary interest), but in addition to this we want to include any blocking factors that will explain variation.

Multi-factor Designs - we will spend at least half of this course talking about multi-factor experimental designs: 2k designs, 3k designs, response surface designs, etc. The point to all of these multi-factor designs is contrary to the scientific method where everything is held constant except one factor which is varied. The one factor at a time method is a very inefficient way of making scientific advances. It is much better to design an experiment that simultaneously includes combinations of multiple factors that may affect the outcome. Then you learn not only about the primary factors of interest but also about these other factors. These may be blocking factors which deal with nuisance parameters or they may just help you understand the interactions or the relationships between the factors that influence the response.

Confounding - is something that is usually considered bad! Here is an example. Let's say we are doing a medical study with drugs A and B. We put 10 subjects on drug A and 10 on drug B. If we categorize our subjects by gender, how should we allocate our drugs to our subjects? Let's make it easy and say that there are 10 male and 10 female subjects. A balanced way of doing this study would be to put five males on drug A and five males on drug B, five females on drug A and five females on drug B. This is a perfectly balanced experiment such that if there is a difference between male and female at least it will equally influence the results from drug A and the results from drug B.

An alternative scenario might occur if patients were randomly assigned treatments as they came in the door. At the end of the study they might realize that drug A had only been given to the male subjects and drug B was only given to the female subjects. We would call this design totally confounded. This refers to the fact that if you analyze the difference between the average response of the subjects on A and the average response of the subjects on B, this is exactly the same as the average response on males and the average response on females. You would not have any reliable conclusion from this study at all. The difference between the two drugs A and B, might just as well be due to the gender of the subjects, since the two factors are totally confounded.

Confounding is something we typically want to avoid but when we are building complex experiments we sometimes can use confounding to our advantage. We will confound things we are not interested in order to have more efficient experiments for the things we are interested in. This will come up in multiple factor experiments later on. We may be interested in main effects but not interactions so we will confound the interactions in this way in order to reduce the sample size, and thus the cost of the experiment, but still have good information on the main effects.