Subsets are groupings that you create in a Project within the larger data sets of samples, features, or genes. Feature and sample subsets are used to restrict analysis to a defined subgroup of features or samples. Up to 100 feature subsets and 100 sample subsets can be defined within a project. Gene subsets can be used for specific analyses, but are not used to restrict the analysis and visualization of sample and feature data.
You can create or edit subsets based on your analysis (see Using Analyses to Form Subsets), or you can create them directly based on a broad range of criteria (see Creating Subsets).
Once a feature or sample subset is created, it can be designated as the Active Subset, which is the one to be viewed in the analysis, or as the Selected Subset, which is one that can be changed or acted on during analysis. The names and number of members for the current Active and Selected Subsets are always displayed in the status bar at the bottom of the Genetrix window.
An Active Subset is a feature or sample subset currently selected for analysis and visualization. Once you have defined a subset you can make it active simply by selecting it in the main icon window (Designating Active Subsets).
The Visualizations and displays performed in Genetrix will include only the Active Subset. When you are working with an Active Subset, not only are the members of that set the only ones included in displays, they are also the only ones included in background calculations such as averaging replicate sets or performing global transformations. Thus where a feature or sample is a member of more than one subset, transformed values associated with it may vary slightly depending on which subset is currently active.
Important: When you have multiple platforms of data in a project, each data platform is limited by its designated Active Subset whether the tab for the platform is selected or not. For example, if you are working with a list of RNAs and want to view the corresponding list of expressions, the expression list will be limited by the currently designated Active Expression Subset.
A Selected Subset is a feature, sample, or gene subset designated to be changed or acted upon. During analysis, when you find a significant group of samples, features, or genes, you can add it to the Selected Subset or remove it. Alternately, you can create a new Selected Subset consisting only of the displayed features or samples (see Using Analyses to Form Subsets). In any Genetrix window where you have the option to save to subset, the subset referred to, is the Selected Subset. For information on designating the Selected Subset, see Managing Subsets.
The Genetrix gene list is based on broadly-known gene lists and their annotations rather than on the array data for a project. The Active gene subset is always all genes. You can designate a Selected gene subset that you can change during analysis as described above. When viewing a gene subset list, you can bring up a list of features associated with those genes, and create a feature subset from the list (see Using Analyses to Form Subsets).
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