ST: Support Trees

Parameter Information



The Support Tree algorithm permits the resampling options to be set separately for the gene tree and the experiment tree.

Tree Construction Options

The Draw Gene Tree and Draw Experiment Tree options allow you to select to construct a gene tree, an experiment tree, or both.

Resampling Options

You can elect to resample either genes or experiments or neither using either a bootstraping or a jackknifing method.

Bootstraping

The matrix is reconstructed such that each expression vector has the original number of values but the values are a random selection (with replacement) of the original values. Values in the original expression vector may occur more than once since the selection uses replacement.

Jackknifing

Jackknifing takes each expression vector and randomly selects to omit an element. This method produces expression vectors that have one fewer element and this is often done to minimize the effect of single outlier values.

Iterations

This indicates how many times the expression matrix should be reconstructed and clustered.

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.

Linkage Method

This parameter is used to indicate the convention used for determining cluster-to-cluster distances when constructing the hierarchical tree.

Single Linkage: The distances are measured between each member of one cluster each member of the other cluster. The minimum of these distances is considered the cluster-to-cluster distance.

Average Linkage: The average distance of each member of one cluster to each member of the other cluster is used as a measure of cluster-to-cluster distance.

Complete Linkage: The distances are measured between each member of one cluster each member of the other cluster. The maximum of these distances is considered the cluster-to-cluster distance.

Support Tree Legend

A legend to relate support tree output colors to % support is displayed by selecting the support tree legend menu item in the main help menu.