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st: Concordance analysis


From   "Wallace, John" <John_Wallace@affymetrix.com>
To   "'statalist@hsphsun2.harvard.edu'" <statalist@hsphsun2.harvard.edu>
Subject   st: Concordance analysis
Date   Mon, 10 Feb 2003 12:41:28 -0800

Title: Message
Hi List Members
 
First of all, my apologies if this gets posted twice.  I originally submitted the email 4 hours ago and I haven't yet seen it appear on the list.
 
On to my question:
A common method of analysis at my company is to take a binary result from one experiment and compare it with the result from another - I'll diagram below.  Each "gene" is independent with respect to the other genes in the experiment. I have heard that these tables can be analyzed for a null hypothesis using Fisher's Exact Test - can Stata be configured to do this?
 
Example
 
Outcomes:
 
Gene ! Exp1 ! Exp2
-----+------+------
2001 !  1   !  1  
2002 !  1   !  1  
2003 !  1   !  0   
2004 !  1   !  0  
2005 !  1   !  1  
2006 !  1   !  1  
2007 !  0   !  1  
2008 !  0   !  0  
2009 !  1   !  1  
2010 !  0   !  0  
 
Concordance Table
     Exp1         
      1    0   Sum
---+----+----+----
   !    !    !   
E 1!  5 !  1 ! 6  
x  !    !    !   
p--+----+----+----
2  !    !    !    
  0!  2 !  2 ! 4  
   !    !    !   
---+----+----+----
S  !    !    !    
u  !  7 !  3 ! 10
m  !    !    !   
 
As I understand it, the null hypothesis is the chance that the table could appear in its observed configuration by chance through random sampling.
 
Thanks for any guidance
 

John Wallace
Research Associate
Affymetrix, Inc
(408)731-5574
3380 Central Expressway 609C
Santa Clara, CA 95051


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