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.