This paper considers statistical issues in the analysis of a designed
experiment to investigate differential gene expression in colon cancer
and normal colon tissue. In this experiment gene expression is measured using
radiolabeling--based array filters. Specific statistical issues arise in
connection with radiolabeling technology, because of the absence of
direct control, which are replaced by empty spots on the filter, and
with designed experiments, because of the opportunity to systematically
quantify important sources of random variation.  Here we consider three
aspects in detail: normalization of expression intensities; shrinkage
estimates of intensity ratios between cancer and normal tissue; and
ranking of genes by the strength of the evidence that they are
differentially expressed. We propose a robust and simple--to--implement
procedures for normalization and shrinkage, that addresses in a
technology--specific way the problem of estimating ratios in presence of
small and noisy denominators. We also discuss a graphical display to
rank genes using a metric based on quantiles of a null distribution
obtained by replicating the array experiment in normal tissue.