[BioC] Signal above negative controls in a two-color experiment - limma?

[John Fowler]

Hello,

I have searched in the FAQ and mailing list, but cannot find an 
answer to my question.  I apologize if this has been asked before.

I have a series of hybs using a long-oligo spotted array for maize, 
and am using two-color (Cy3 & Cy5-labelled) targets.  I would like to 
generate a list of probes that detect signal that is 'above 
background' for each target - that would be, significantly greater 
than signal detected by the negative control probes on the array 
(Aliens and Human sequences).  These would hopefully identify a set 
of genes that are expressed vs not-detectably-expressed in my tissues 
of interest.

I have a loop design, and am using limma to identify differentially 
expressed genes.  Is it possible to use limma to also do the analysis 
I suggested above?  I assume that this would involve using the 
separate channel functions of limma, but am unclear on how to 
approach it.

Many thanks,
John

-- 
John Fowler				Associate Professor
Botany and Plant Pathology (BPP) Dept.
2082 Cordley Hall                        Phone: (541) 737-5307
Oregon State University                  FAX: (541) 737-3573
Corvallis, OR  97331-2902  USA	   	 Email: fowlerj at science.oregonstate.edu