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.
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.