I am hoping someone can review my model and see if I am using the block argument in lmFit to correctly achieve a paired test. I have 12 samples made up of 4 people, each person is sampled 0hr, 4hr, and 22hr after exposure. The 12 slides are affy. I want to do a paired analysis using lmFit. My data looks like this: slide h0 h4 h22 person 1 1 0 0 1 2 0 1 0 1 3 0 0 1 1 4 1 0 0 2 5 0 1 0 2 6 0 0 1 2 7 1 0 0 3 8 0 1 0 3 9 0 0 1 3 10 1 0 0 4 11 0 1 0 4 12 0 0 1 4 design <- model.matrix(~ -1+factor(c(1,2,3,1,2,3,1,2,3,1,2,3))) colnames(design) <- c("h0","h4","h22") fit <- lmFit(exprs(exp1.all.gcrma), design, block=c(1,1,1,2,2,2,3,3,3,4,4,4)) cont.matrix <- cbind(h.22.0=c(-1,0,1), h.22.4=c(0,-1,1), h.4.0=c(-1,1,0)) fit2 <- contrasts.fit(fit, cont.matrix) fit2 <- eBayes(fit2) Am I using the block argument correctly? Perhaps an easier question would be to ask how to set up the design and contrast matrix to get a simple paired t-test type of analysis. base 2.0.1 datasets 2.0.1 utils 2.0.1 grDevices 2.0.1 graphics 2.0.1 stats 2.0.1 methods 2.0.1 tools 2.0.1 Biobase 1.5.0 reposTools 1.5.1 affy 1.5.8 xtable 1.2-4 limma 1.8.6 matchprobes 1.0.12 gcrma 1.1.1 qvalue 1.1 siggenes 1.2.11 Thanks very much for any help or pointers. Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html