The Miscellaneous tab is used for some additional filtering options, depending on the search module.
For instance, the Fetch section is used to specify what results are returned in the Ranked project search (Raw p-values, adjusted p-values, fold changes, estimates, Max(LSMean), and Odds ratio).
The Scoring System section is used to set the scores for the bins for Ranked Variable List search. The search is broken into three bins, and the user can set the score at which a test/project is counted for that bin, along with the weight for the score. By default, the bins are set to scores of 99, 95, and 90 with weights of 10, 2, and 1.
The Limit section can limit the number of searched variables if filters are applied. Usually, this does not matter, but in some rare cases, the user may want to increase the number of variables that are searched. In addition, the user can set the number of profiles that are fetched (Ranked projects), or the number of total records that are returned.
Finally, checked by default, is the option to automatically download items (like Array Studio lists) when double-clicking on a project.