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List:       bioconductor
Subject:    [BioC] P>1 (edgeR and sage.test)
From:       Naomi Altman <naomi () stat ! psu ! edu>
Date:       2010-06-30 20:53:40
Message-ID: 6.2.3.4.2.20100630165124.0254e7d0 () imap ! stat ! psu ! edu
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Both the Fisher exact test and sage.test (in sagenhaft) can produce 
p-values slightly bigger than 1.  This can mess up down-stream 
analyses (like using qvalue, e.g.). Perhaps the functions could be 
modified to truncate the p-values at 1.0.

Thanks,

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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