DNA microarray experiments, a well-established experimental technique, aim at
understanding the function of genes in some biological processes. One of the
most common experiments in functional genomics research is to compare two
groups of microarray data to determine which genes are differentially
expressed. In this paper, we propose a methodology to estimate the proportion
of differentially expressed genes in such experiments. We study the performance
of our method in a simulation study where we compare it to other standard
methods. Finally we compare the methods in real data from two toxicology
experiments with mice.Comment: Published at http://dx.doi.org/10.1214/074921707000000076 in the IMS
Lecture Notes Monograph Series
(http://www.imstat.org/publications/lecnotes.htm) by the Institute of
Mathematical Statistics (http://www.imstat.org