For presentation and publishing purposes, it is often convenient to assign names to clusters and make them appear in the graphic windows. Typically, a cluster name reflects the biological function of the genes in the cluster, or the general trend of the expression levels of the genes in the cluster (such as "periodic", "ascending", "controlled by X", etc.). ArrayMiner allows you to assign names to clusters, and displays those names in most graphical representations, in particular the 2D and 3D view of your clustering solution.
    Coupled with the possibility of saving the various views into image files, cluster names provide a convenient presentation tool.

    To assign a name to a cluster, right-click on the cluster's thumbnail in the Profiles Header in the main graphic window, and select the "Set cluster name" in the popup menu. To remove a name, simply set an empty name. Note that two clusters cannot have the same name. The set of outliers (Gaussian clustering only) cannot be assigned a name.
    The cluster names are shown in most windows automatically, with the exception of the 2D and 3D views. In the 2D and 3D views, the cluster names are shown/hidden together with the cluster centers. To show/hide the cluster names, show/hide the cluster centers using the "Names" button in the Button Panel in the 2D or 3D view.
    Cluster names are saved with and subsequently retrieved from an AMG file.

    Since a cluster name identifies a cluster, and a cluster is a set of genes, it follows that if the contents of (the set of genes in) a named cluster changes, the name is no longer relevant. Accordingly, a cluster's name is removed when the cluster changes, which may (and ususally does) happen during the clustering process. The best time to assign cluster names is therefore at the end of a clustering process.

    When ArrayMiner is run from GeneSpring, cluster names are fully utilised:

• Assigning cluster names before returning a clustering solution to GeneSpring will make ArrayMiner use the assigned names in the classification returned to GeneSpring - the assigned names are thus used in the resulting GeneSpring classification
• When viewing a GeneSpring classification with "ArrayMiner View", ArrayMiner uses the names in the GeneSpring classification as cluster names