[BioC] microarray and t.test

[Sean Davis]

On 3/6/06 1:23 PM, "Roth, Richard" <rroth at neurocrine.com> 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 (at minimum) for
> each test, possibly in another matrix.  Can anyone help me with the t.test
> setup for this analysis?

Look at the multtest to do what you are asking.  However, there are more
powerful tests for microarrays included in the siggenes and limma packages,
as well as several others.  Each has a vignette or other documentation to
get you going.  Limma has a complete user guide that includes and example of
affy data in two classes, if I recall correctly.

Sean