Package ubic.erminej

Class Summary

Class	Description
Analyzer
classScoreCMD	Run ermineJ from the command line (or fire up the GUI).
ClassScoreSimple	Simple API to run ermineJ analyses, using Strings as the initial representations.
ErmineJGui	Main for GUI
ResultsFileReader	Load results from a file.
ResultsPrinter
Settings	Basically a wrapper around a Commons Configuration object.
SettingsHolder	Holds settings for retrieval but doesn't allow changing them (with a couple of exceptions) or saving them.

Enum Summary

Enum	Description
SettingsHolder.GeneScoreMethod	For the gene set resampling method, how are scores computed for the group?
SettingsHolder.Method	Which gene set scoring method to use.
SettingsHolder.MultiProbeHandling	What to do when there are multiple values for a gene.
SettingsHolder.MultiTestCorrMethod	How to correct for multiple tests.