Categorical data, as the name suggests, are data that can be grouped into specific categories.
In a biological experiment, categorical factors refer to variables that can fall into distinct categories. For example, in a given experiment, the type of media you grow your cells in can be, for example, LB media or M9 Minimal Media. You might want to investigate two or more categorical levels. By using the different categories and observing the effects they have, you can gain insights into the impact that a specific category has on the behaviour of your biological system.
For example, if you are performing a media optimisation experiment, and want to investigate the effect that the type of carbon source - Glucose or Glycerol -, has on the performance of your media, when at a fixed concentration, you should consider the carbon source a categorical factor. Unlike numeric factors, what you are studying here is not the effect of the concentration of your carbon source, but the choice of the carbon source itself.
In Synthace, we handle how to treat your factors automatically, based on the context in which they are defined. Factors that are applied to the Diluent To Use parameter in the Make Mixtures or Mix Onto elements are automatically treated as categorical (Figure 1). Another example when factors are automatically treated as categorical, is when defining liquid components that form part of a mixture, within the Mixture Composition parameter in the Make Mixtures or Mix Onto elements (Figure 1).
Figure 1. Examples of categorical factors in Synthace. The most common categorical factors described in Synthace workflows are the diluent type to use to top up a reaction to a final target volume, and the choice of a liquid component at a fixed volume or concentration to add to a mixture.
Another common example of a categorical factor in biological experiments is when you want to test the effect of two formulations of the same compound, often from two or more consumable vendors. For example, if you are optimising a molecular biology process you might want to test the same DNA cutting enzyme manufactured by two or more different companies, to assess which formulation has an optimal effect on your system (Figure 2).
Figure 2. Example of categorical factors in Synthace. Sometimes you might want to test the same component in your mixture but from different consumable vendors. Here, you might use a categorical factor to describe the three consumable vendors.
To learn how to define a categorical diluent factor, click here.
To learn how to define a categorical mixture component factor, click here.
To learn how to define a custom categorical factor, click here.
To learn about other types of factors, click here.