Hypothesis testing is an approach to statistical inference that is routinely taught and used. It is based on a simple idea: develop some relevant speculation about the population of individuals or things under study and determine whether data provide reasonably strong empirical evidence that the hypothesis is wrong. Consider, for example, two approaches to advertising a product. A study might be conducted to determine whether it is reasonable to assume that both approaches are equally effective. A Type I error is rejecting this speculation when in fact it is true. A Type II error is failing to reject when the speculation is false. A common practice is to test hypotheses with the type I error probability set to 0.05 and to declare that there is a statistically significant result if the hypothesis is rejected.
There are various concerns about, limitations to, and criticisms of this approach. One criticism is the use of the term significant. Consider the goal of comparing the means of two populations of individuals. Saying that a result is significant suggests that the difference between the means is large and important. But in the context of hypothesis testing it merely means that there is empirical evidence that the means are not equal. Situations can and do arise where a result is declared significant, but the difference between the means is trivial and unimportant. Indeed, the goal of testing the hypothesis that two means are equal has been criticized based on the argument that surely the means differ at some decimal place. A simple way of dealing with this issue is to reformulate the goal. Rather than testing for equality, determine whether it is reasonable to make a decision about which group has the larger mean. The components of hypothesis-testing techniques can be used to address this issue with the understanding that the goal of testing some hypothesis has been replaced by the goal of determining whether a decision can be made about which group has the larger mean.
Another aspect of hypothesis testing that has seen considerable criticism is the notion of a p-value. Suppose some hypothesis is rejected with the Type I error probability set to 0.05. This leaves open the issue of whether the hypothesis would be rejected with Type I error probability set to 0.025 or 0.01. A p-value is the smallest Type I error probability for which the hypothesis is rejected. When comparing means, a p-value reflects the strength of the empirical evidence that a decision can be made about which has the larger mean. A concern about p-values is that they are often misinterpreted. For example, a small p-value does not necessarily mean that a large or important difference exists. Another common mistake is to conclude that if the p-value is close to zero, there is a high probability of rejecting the hypothesis again if the study is replicated. The probability of rejecting again is a function of the extent that the hypothesis is not true, among other things. Because a p-value does not directly reflect the extent the hypothesis is false, it does not provide a good indication of whether a second study will provide evidence to reject it.
Confidence intervals are closely related to hypothesis-testing methods. Basically, they are intervals that contain unknown quantities with some specified probability. For example, a goal might be to compute an interval that contains the difference between two population means with probability 0.95. Confidence intervals can be used to determine whether some hypothesis should be rejected. Clearly, confidence intervals provide useful information not provided by testing hypotheses and computing a p-value. But an argument for a p-value is that it provides a perspective on the strength of the empirical evidence that a decision can be made about the relative magnitude of the parameters of interest. For example, to what extent is it reasonable to decide whether the first of two groups has the larger mean? Even if a compelling argument can be made that p-values should be completely abandoned in favor of confidence intervals, there are situations where p-values provide a convenient way of developing reasonably accurate confidence intervals. Another argument against p-values is that because they are misinterpreted by some, they should not be used. But if this argument is accepted, it follows that confidence intervals should be abandoned because they are often misinterpreted as well.
Classic hypothesis-testing methods for comparing means and studying associations assume sampling is from a normal distribution. A fundamental issue is whether nonnormality can be a source of practical concern. Based on hundreds of papers published during the last 50 years, the answer is an unequivocal Yes. Granted, there are situations where nonnormality is not a practical concern, but nonnormality can have a substantial negative impact on both Type I and Type II errors. Fortunately, there is a vast literature describing how to deal with known concerns. Results based solely on some hypothesis-testing approach have clear implications about methods aimed at computing confidence intervals. Nonnormal distributions that tend to generate outliers are one source for concern. There are effective methods for dealing with outliers, but technically sound techniques are not obvious based on standard training. Skewed distributions are another concern. The combination of what are called bootstrap methods and robust estimators provides techniques that are particularly effective for dealing with nonnormality and outliers.
Classic methods for comparing means and studying associations also assume homoscedasticity. When comparing means, this means that groups are assumed to have the same amount of variance even when the means of the groups differ. Violating this assumption can have serious negative consequences in terms of both Type I and Type II errors, particularly when the normality assumption is violated as well. There is vast literature describing how to deal with this issue in a technically sound manner.
A comparative analysis of cell-type adjustment methods for epigenome-wide association studies based on simulated and real data sets
