QTC: QT_Cluster

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.

Maximum Cluster Diameter

Cluster Diameter is related to the overall variability between the member elements within a cluster. Maximum Cluster Diameter is a constraint on that variance such that all formed clusters must have a diameter (variability) smaller that the entered maximum. Increasing the maximum diameter tends to make larger and more variable clusters and decreasing the maximum diameter tends to produce smaller less variable clusters.

Minimum Cluster Population

The minimum number of elements required to be present in order to form a cluster. For instance a Minimum Cluster Population of 10 insures that all formed clusters will have at least 10 members.

Hierarchical Clustering

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