KMC: K-Means/K-Medians
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.
Euclidean Distance and Pearson Correllation tend to be the most frequently used options.
An appendix in the MeV manual describes the distance metrics offered in MeV.
Means/Medians option
The Means or Medians option indicates whether each cluster's centroid vector
should be calculated a mean or a median of the member expression patterns.
Number of Clusters
This positive integer value indicates the number of clusters to be created.
Note that FOM can be used to estimate an appropriate value.
Number of Iterations
This positive integer value is the maximum number of times that all the elements in the data set
will be tested for cluster fit. On each iteration each element
is associated with the cluster with the closest mean (or median).
Note that the algorithm will terminate when either no elements
require migration (reassignment) to new clusters or when the maximum number of
iterations has been reached.
Hierarchical Clustering
This check box selects whether to perform hierarchical clustering on the elements in each cluster
created.