R help - Mar 2006 - t.test question

Hi, I have a data matrix of gene expression data from two groups that I would
like to compare using the t-test.  The data has been processed using RMA and
transformed using log2.  I would like to compare the two groups for each gene
(N=10,000 genes) and have a result that lists the p-value for each test.  Can
anyone help me with the t.test setup for this analysis?

Thanks, Rich

Rich Roth, PhD
Senior Scientist
Molecular Medicine
Neurocrine Biosciences
858-617-7204


-------------- next part --------------
"MMS <neurocrine.com>" made the following
 annotations on 03/06/2006 10:04:49 AM
------------------------------------------------------------------------------
This email may contain confidential and privileged material ...{{dropped}}

Roth, Richard wrote:
> Hi, I have a data matrix of gene expression data from two groups that
> I would like to compare using the t-test.  The data has been
> processed using RMA and transformed using log2.  I would like to
> compare the two groups for each gene (N=10,000 genes) and have a
> result that lists the p-value for each test.  Can anyone help me with
> the t.test setup for this analysis?
Take a look at the limma package in BioConductor. You will be able to do 
what you want much faster than using e.g., t.test(). There is an 
extensive user's guide that should help you figure out what to do.

HTH,

Jim



> 
> Thanks, Rich
> 
> Rich Roth, PhD Senior Scientist Molecular Medicine Neurocrine
> Biosciences 858-617-7204
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> 
> ______________________________________________ 
> R-help at stat.math.ethz.ch mailing list 
> https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the
> posting guide! http://www.R-project.org/posting-guide.html

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623