Issue with gominer.Fisher which is used by org/campagnelab/goby/stats/FisherExactTestCalculator.java

[pgrt]

Hello,

In version 3.3.1 of Goby, I see gominer.Fisher is used to compute p-values of Fisher tests in org/campagnelab/goby/stats/FisherExactTestCalculator.java.

During the test org.campagnelab.goby.stats.TestStatistics.testTwoStats, the p-value of the Fisher test associated to the table
322777 318050
160397 151279
is computed, and the p-value given by gominer.Fisher is 1. Yet, passing this table to R (fisher.test) or even to https://www.langsrud.com/fisher.htm gives a p-value that is lower than 1.E-16. So the test testTwoStats should be changed as it should not expect a p-value of 1 for the Fisher test.

Enclosed is a patch which would avoid needing gominer and use DistLib (https://sourceforge.net/projects/statdistlib/) instead. It needs a review before maybe being included, still.

computing_fisher_pvalue_hypergeom.txt

Best regards,

--
Pierre