Hi there, I am analyzing microarray data. We use the 2-step mixed model analyses proposed by Wolfinger et al (2001). One phenomena that we observe is that after analyses we plot the p-values. The p-values do not follow an uniform distribution with more differentially expressed genes at the 5 % significance level. We observe fewer genes at the 5% significance level and the percent of observations at higher p-values increase. I am curious to know if other groups have seen this or other types of distributions for the p-value. How do you deal with this and how do you analyze the data? Thanks, Renate Renate T.E. van Dorp, PhD. Center for Animal Functional Genomics Department of Animal Science B212 Anthony Hall Michigan State University East Lansing, MI 48824 Office (517) 432-1379 Lab (517) 353-9815 FAX (517) 353-1699