There are a few terms used throughout the SeqMonk documentation which it is useful to understand before using the program.
A data set refers to a set of regions imported from a single file. These regions should all come from a single biological condition, but they may not be the only regions to come from that condition.
A data group is a way of merging together two or more DataSets. When data from one biological sample is present in more that one DataSet you can use a DataGroup to combine them together. A Data Group does not copy the original data it just transparently aggregates two or more data sets, but it will store its own quantitation information.
A replicate set is a way of grouping together DataSets or DataGroups which come from different instances of the same biological condition. As with the Data Group it does not copy any sequence data which is just taken from the underlying data sets, and it does not store its own quantiation information, it merely averages the quantitations present in the underlying data sets or groups.
A Data Store simply refers to either a data set, data group or replicate set in a situation where it doesn't matter which one you have. Most analyses and displays in SeqMonk operate on Data Stores and they work equally well with either Data Sets, Data Groups or replicate sets.
A probe is a genomic region in which a quantitated measurement can be made. Probes can be defined in a variety of ways using the various Probe Generators available. After quantitation each probe will have a value for each Data Store.
A Probe Set is a collection of Probes. You can have only one active Probe Set in your analysis and this will be the same for all Data Stores. Whilst it is possible to regenerate your Probe Set, doing this will cause you to lose all of the data corresponding to the Probe Set being replaced.
A Probe List is a subset of your Probe Set. Probe Lists are produced by the various Filters available within SeqMonk. Each probe in a Probe List can have a value associated with it. For example following a statistical filter the Probe List generated might store the p-value for each Probe in the list.