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.