Q: If the limitations of the study cannot be avoided, how can they be minimized?

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Interesting, relevant question. Much will depend on what the limitations are, and some can be serious enough: so serious that it is futile to justify or minimize them. Examples of such limitations include a very small sample size, non-random sampling, and unreliable methods of chemical analysis. One possibility in such cases is to see whether the study can be presented not as original research but as a case study, because the observations and findings of a case study are not expected to lead to broad generalizations. (For a related example from the forum, go through this question: Will my paper be regarded as an original research article or a case study?)

Whether a given aspect or feature of a study is a limitation also depends on the objective of the study. A study that seeks to analyze the commuting habits of people in a large city, for example, will need a much larger sample incorporating many origins and destinations, different modes of transport, different times of the day and different days of the week, and several different categories of commuters (men, women, children, young or old, and so on). A sampling method that fails to yield a representative sample will then be a serious limitation. On the other hand, a more specific study, with limited scope – to analyze the modes of transport used by pupils in one school, for example – may not require a large and diverse sample.

The strategy to minimize limitations, therefore, should focus on convincing reviewers that the limitations do not affect the conclusions of the study by showing that the methods are appropriate and that the logic is sound. As an author, you should emphasize that the data on which the conclusions are based are valid; that the statistical methods, if any, used for drawing inferences from the data are adequate; and that studies with similar limitations have been published before. It is important not to gloss over the limitations (not to make them seem unimportant, not to ignore them, or not to represent them to mislead), but to admit them openly and at the same time show how they do not affect the main conclusions of the study. If appropriate, you can indicate how a future study can be planned to overcome the limitations of the present one.

Note that these are only general strategies: more specific advice can be given only for specific limitations. For more insights, you may refer to these resources: