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.