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.