Qualitative data are commonly collected in higher, graduate and postgraduate education, however, perhaps especially in the quantitative sciences, utilization of these qualitative data for decision-making can be challenging. A method for the analysis of qualitative data is the degrees of freedom analysis (DoFA), published in 1975. Given its origins in political science and its application in mainly business contexts, the DoFA method is unlikely to be discoverable or used to understand survey or other educational data obtained from teaching, training or evaluation. This article therefore introduces and demonstrates the DoFA with modifications specifically to support educational research and decision-making with examples in bioinformatics. DoFA identifies and aligns theoretical or applied principles with qualitative evidence. The demonstrations include two hypothetical examples, and a case study of the role of scaffolding in an independent project (capstone) of a graduate course in biostatistics. Included to promote inquiry, inquiry-based learning and the development of research skills, the capstone is often scaffolded (instructor-supported and therefore, formative), although it is intended to be summative. The case analysis addresses the question of whether the scaffolding provided for a capstone assignment affects its utility for formative or summative assessment. The DoFA is also used to evaluate the relative efficacies of other models for scaffolding the capstone project. These examples are intended to both explain this method and to demonstrate how it can be used to make decisions within a curriculum or for bioinformatics training.