Date:         Mon, 17 Dec 2007 15:51:18 -0600
Reply-To:     Mary <mlhoward@avalon.net>
Sender:       "SAS(r) Discussion" <SAS-L@LISTSERV.UGA.EDU>
From:         Mary <mlhoward@AVALON.NET>
Subject:      Re: Performing thousands of tests automatically
Comments: To: Ron Do <rondo@HOTMAIL.COM>
Content-Type: text/plain; charset="iso-8859-1"

Ron,

What is the disease that you are looking at?

You may want to take a look at the paper that ran over 100,000 SNP's for some discussion of significance levels.  It is

Complement Factor H Polymorphism in Age-Related Macular Degeneration, by Robert J. Klein, Caroline Zeiss, Emily Chew.  www.sciencemag.org, SCIENCE VOL 308 15 April 2005 page 385-389.

However, that particular study only found significance on CFH and missed a later found significance on LOC387715, perhaps because the significance level was set so low. 
 
Mary Howard

Research Assistant III

Dept. of Ophthalmology

Univ. of Iowa Hospitals and Clinics

  ----- Original Message ----- 
  From: Ron Do 
  To: SAS-L@LISTSERV.UGA.EDU 
  Sent: Monday, December 17, 2007 3:40 PM
  Subject: Re: Performing thousands of tests automatically


  Thanks everyone for the responses.  I will try some of the suggestions and
  see how they work.

  Mary is right, this is for a genome-wide association study using over
  100,000 markers.  There are some genetics programs that can handle this
  data, but I'm interested in applying a mixed effects model to analyse this
  data and hence am curious if SAS is capable of doing this.

  I'll let you all know how it goes.

  Cheers,
  Ron