Dear Bioconductor, I'd like to know if I'm heading in the right direction with my analysis and to see if anyone can answer a question about contrasts. My data set involves two types of graft implants (allograft and isograft) and three different time points (4, 14 and 25 days) with 5 replicates at each combination. The microarray platform is the Affy 430A array and I used the gcrma package to process my data set (indicated below) > mouse.gcrma Expression Set (exprSet) with 22690 genes 30 samples phenoData object with 2 variables and 30 cases varLabels Gtype: read from file Gday: read from file I have set up a model with no variables lm.empty <- function(y) lm(y ~ 1) lm.e <- esApply(mouse.gcrma,1,lm.empty) , a model with only time point effect lm.day <- function(y) lm(y~Gday) lm.d <- esApply(mouse.gcrma,1,lm.day) and a full model lm.full <- function(y) lm(y~Gtype*Gday) lm.f <- esApply(mouse.gcrma,1,lm.full). I have used the anova function to get p-values for differences between empty/full and day/full and then used multtest to account for multiple comparisons. Now, I'd like to start running some contrasts to see the effects at particular graft type/day combinations (ie 14 day allografts) and also look at fold changes. I think both of these functions are possible within the factDesign package, but I'm not sure how to input the second and the third parameters in the par2lambda function. If there's anyone who can give me some direction on this, I would greatly appreciate it. Thanks, Jeff Lande Graduate Student - University of Minnesota [[alternative HTML version deleted]]