FISHER: Fisher's Exact Test for 2x2 Tables

(c) Copyright March 1998 by Jianzhi Zhang and the Pennsylvania State University.
Permission is granted to copy this document provided that no fee is charged
for it and that this copyright notice is not removed.  BN-BS is distributed
free of charge by

        Jianzhi Zhang
        Institute of Molecular Evolutionary Genetics
        and Department of Biology
        322 Mueller Laboratory
        The Pennsylvania State University
        University Park, PA 16802, USA

        Telephone: 814-8657030
        Fax: 814-8637336
        Email: zhang@imeg.bio.psu.edu

        Suggested citation:

        Zhang J, Rosenberg HF, Nei M (1998)  Positive Darwinian selection after
        gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci.
        USA 95:3708-3713.


1. Introduction
        FISHER is designed for testing independence for a 2x2 table such as  

                                   ------------|--
           			    a        b | a+b
           			    c        d | c+d
          		           ------------|--   
				   a+c     b+d |

In other words, it answers the following question: Given two-way tables with the same
fixed margin totals as the observed one, what is the chance of obtaining the observed
cell frequencies a, b, c, and d and all cell frequencies that represent a greater 
deviation from expectation (see Sokal and Rohlf 1995).


2. Installation
        First make sure that the diskette you have received contains the
following files.

    fisher.c          (source code)
    fisher.exe        (executable file)    
    
        To install FISHER on your computer's hard disk drive ("C" drive
given here, for example), you should create a directory where the files of
this package will be present.  To do this, type the following
                c:\md FISHER  (Enter)

        To copy the FISHER files onto your hard disk drive, insert the
floppy disk containing the programs into your floppy drive ("A" drive given
here, for example).  Then, enter the following command
                c:\copy a:*.* c:\FISHER\*.*  (Enter)

4.  Computation
        To compute the p(robability) value, type
              c:\FISHER\fisher
        
        You will be asked to input four integers for the four cells of the 2x2 table.
And the probability (p) will show up instantly.