[BioC] necessity of moderated t statistic and false discoveries for small predefined gene list?

[Richard Friedman]

Dear Bioconductor  List.

	I am using Limma to analyze differential expression between 2  
conditions on an Affy chip.
My experimental collaborator asks for the differential  expression of  
10 predefined genes.

A, Should I correct for false discoveries based upon all of the genes  
on the chip?
B. If not, should I correct for false discoveries just for the  
probeids for the 10 predefined
genes?
C. Should I use the moderated t-statistic or just use an unmoderated t- 
test for those 10
genes.

Thanks and best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

"School is an evil plot to suppress my individuality"

Rose Friedman, age15