PTM: Pavlidis Template Matching

Parameter Information


Template Selection Tabs

The five tabbed panels at the top of the dialog select to view candidate templates from various sources.

The Gene Template tab provides a list of genes in the data set and their expression profile graphs. Selection of elements in the list display the expression pattern for that gene.

The Gene Cluster Template tab provides a list and view of templates which are the mean values of stored (colored) clusters.

The Experiment Template, and Experiment Cluster Template tabs provide the same functionality but use experiment templates.

The Saved Template tab provides an interface for loading gene and experiment templates. Templates loaded from files will populate a list from which a template may be selected.

A button in each of these areas is used to select the displayed template for matching.

Threshold Parameters

Use Absolute R

Using this option will select expression patterns that are either positively or negatively correlated with the template.

Use Threshold R

This option will indicate that the threshold value for determining a match is the R value between the expression vector and the template.

Use Threshold p-Value

This option will indicate that the threshold value for determining a match is the p value on R between the expression vector and the template.

Threshold Input Value

This is either a supplied value for R or a p-value ranging from 0.0 to 1.0. R values closer to 1.0 are more stringent. p-values closer to 0 are more stringent.

Save Template

This button launches a file browser to allow the user to save the current template to a tab delimited text file. These files can be loaded from the Saved Template tab interface.

Hierarchical Clustering

This check box selects whether to perform hierarchical clustering on the elements in the resulting matched and unmatched element sets.