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    HOW TO COMPILE:
    1. [IN UNIX]under the directry ermineJ/java_proj, type in 'make' to compile the program.
    2. [IN DOS]under the directry ermineJ/java_proj, type in 'makerun' to compile the program.

    HOW TO USE:
    1. [IN UNIX]under the directry ermineJ/java_proj, type in 'make run' to start the program, a GUI will pop up in seconds.
    2. [IN DOS]under the directry ermineJ/java_proj/sources, type in 'run' to start the program, a GUI will pop up in seconds.
    3. In the GUI: From the top of the GUI, click 'Browse...' to choose import files(for GUI details, see GUI DESCRIPTION section below).
    4. Check or change all other options by your need, then click 'ok' button to start computation.
    5. A confirmation window will pop up and tells you the setting for this computation, check again and push 'ok' if everything is correct;
       click 'no' to go back one step.
    6. After the 'ok' button be clicked, a progress bar will pop up during the computation, wait until the progress bar gone, then the result
       will be stored in your designated folder.

    GUI DESCRIPTION:
    1. Pval File -- the list of genes and corresponding p-palues
    2. Affy GO File -- the list of Gene Ontology(GO) classes and correponding genes
    3. Destination File -- assign a name for the output file
    4. Go Biological Names File -- the list of Gene Ontology classes and correponding descriptions
    5. Unigene File -- the list of unigene tags and corresponding genes
    6. Weight -- check if the genes in same unigene catagory be combined and considered as one gene.
    7. Methods:
       Mean -- Take the mean of random selected samples to build distributions for pval calculations
       Quantile -- Take the quantile of random selected samples to build distributions for pval calculations.
    8. Number of Iterations -- Determine how many random samples to take to built up each distribution.
    9. Quantil -- Set the portion of quantile, range 0~100. For Median Method, set quantile equals 50.
    10.P-value -- Define the threshold for hyper geometric distribution computation.
    11.Max/Min class size -- Choose the size range of target GO classes.

    OUTPUT FILE:
    The columns in output file are ordered as:
    1. class name -- the description of each GO class, parenthesized by its GO number.
    2. size -- the actual size, means how many genes in the Pval File are belong to this GO class.
    3. rawscore -- the rawscore of this GO class.
    4. pval -- the class p-value, computed buy median/mean method.
    5. virtual size -- only shown if the 'Weight' method is applied. Means the number of unigenes belongs to this GO class.
    6. hyper pval -- the hyper geometric distribution p-value of this GO class.
    7. roc rate -- the roc score of this GO class.
    8. rocpval -- roc method p-value of this GO class.

Last modified: Tue Dec 17 15:08:15 EST 2002