CAST: Cluster Affinity Search Technique

Parameter Information


Sample Selection

The sample selection option indicates whether to cluster genes or experiments.

Distance Metric Selection

This area allows the selection of the metric to be used to assess gene-to-gene or sample-to-sample distances. The initial metric displayed (choosen) corresponds to the global setting in the Multiple Array Viewer's 'Metrics' menu. Alterations to the chosen metric in this dialog will only alter the metric used for the current algorithm run. The global setting in the main 'Metrics' menu will remain unchanged.

An appendix in the MeV manual describes the distance metrics offered in MeV.

Threshold

The threshold parameter is a value ranging from 0.0 to 1.0 which is used as a cluster affinity threshold. Each expression element will have an affinity for the current cluster being created based on it's relationship to the elements currently in the cluster. If that affinity is greater than the supplied threshold the gene is permitted to be a member of the cluster.

Note that thresholds near 1.0 are more stringent and tend to produce many clusters with rather low variability. Conversely, using a lower threshold will produce fewer, more variable clusters. A balance by trail-and-error should be found between these extremes.

Note that in the algorithm expression elements are repeatedly tested for their affinity to the cluster being formed. In that way elements can be added or subtracted based on the current cluster membership.

Hierarchical Clustering

This check box selects whether to perform hierarchical clustering on the elements in each cluster created.