RP: Rank Products

Parameter Information


Rank products is a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments.

Group Assignments

Group Selection Controls

This set of buttons determines which experiments on which to run the analysis. If an experiment is unchecked it will be ignored for the purposes the analysis.

Note that groups A and B must each have at least two members following the assignment.

Save Grouping

The save grouping button allows you to save the grouping to file. This is particularly useful when there are many experiments.

Load Grouping

This button allows you to select and load a saved grouping.

Reset

The reset button returns all of the group selection control buttons to Group A, the initial state.

Significance Level Parameters

Significance levels are determined by random permutations.
Choose a value for the number of random permutations, 100 is the default.
Choose a value (between 0 and 1) for the alpha value or critical p-value. If permutations are used, two buttons allow you to select to permute the values a number of times indicated or to permute the values a number of times equal to the maximum number of permutations possible.

False discovery control

Under this option, with confidence of (1 - alpha), the number or proportion of false positives in the significant gene list should not exceed the input value.

Hierarchical Clustering

This check box selects whether to perform hierarchical clustering on the elements in each cluster created.