[BioC] Gene selection: association with linear response and correction for multi test

[david neil hayes]

I am interested in selecting genes associated with a linear outcome (drug 
dose) and including adjustments for multiple testing/false discovery.  As an 
example, the Excel version of SAM, for example, has an implementation where 
the delta statistic is based on the linear regression coefficient.

Am I correct, this response type is not supported in either the development 
or current release of siggenes?

I re-reviewed siggenes and reviewed the limma package (with which I am less 
familiar), as well as some of the on-line Bioconductor tutorials, and it was 
not clear to me that there was an application that I could select as a 
"standard" method (or at least a method with published references) of 
selecting genes associated with a linear response.

This strikes me as a question similar to one that has been asked many times 
before, but on review of the mail archives, I couldn't find an answer.  I am 
sure I am missing something simple.  Any suggestions?

Neil Hayes
UNC Chapel Hill