[BioC] microarray and t.test

[Hassane, Duane]

Rich,

I've sometimes suggested the mt.wrapper function which will get you exactly
what you want quickly (from the webbioc package by Colin Smith).  As a
wrapper, it integrates the functionality in multtest.  That said, you will
be better off in the long term to look at multtest itself and the other more
powerful packages that Sean mentioned.  

Best,

Duane

-----Original Message-----
From: Roth, Richard [mailto:rroth at neurocrine.com]
Sent: Monday, March 06, 2006 1:24 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] microarray and t.test


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 (at
minimum) for each test, possibly in another matrix.  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


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