RN: Relevance Networks
Parameter Information
Sample Selection
The sample selection option indicates whether to cluster genes or experiments.
Use Permutation Test
This check box is used to indicate that the minimum threshold R^2 value should be
selected based on a distribution constructed from element to element R^2 values
derived following permutation of the expression vectors.
Min Threshold
This value ranging from 0 to 1.0 indicates
the smallest R^2 possible between two elements to permit a link between the
elements in a subnet.
Max Threshold
This value ranging from 0 to 1.0 indicates
the greatest R^2 possible between two elements to permit a link between the
elements in a subnet.
Use Filter
This option allows the user to filter out elements with little dynamic change thus
removing flat or uninteresting elements.
A measure of entropy is used to rank the elements. The percentage value
entered (1 to 100) indicates what percentage of the elements to retain
for the construction of the network. A value of 25 will retain the 25%
of elements having the greatest entropy.