Hi can someone take a look at this and see if my design is correct?  What I'm trying to achieve is similar to a 2-way ANOVA main effect and interactions with LIMMA.  

I would like to look at the main effect of gene, time and interaction as well as comparison of gene regardless of time. Sorry if this has been asked before, but  I was hoping to get some confirmation.  

thanks!

ds <- read.table(header = TRUE, text =
                 "id gene time
                   1 gfp t24
                  2 ko   t24
                  3 gfp t75
                  4 ko t75
                 ")

ft <- paste(ds$time,ds$gene,sep=".")

ft <- factor(ft)
ft
design2 <- model.matrix(~0+ft)
colnames(design2) <- levels(ft)
design2

cont.matrix <- makeContrasts(
  gene.main = "(t24.ko + t75.ko)/2 - (t24.gfp + t75.gfp)/2", 
  time.main = "(t75.gfp + t75.ko)  /2  - (  t24.gfp +  t24.ko) /2 ",
  Interaction="(t24.ko - t75.ko) - (t24.gfp - t75.gfp)",
  gfp.vs.ko = " (t24.ko + t75.ko) - (t24.gfp + t75.gfp) "
  ,levels=design2)

You need to divide by two for the last contrast as well, but otherwise seems ok to me. Plus I don't think you want to use quotes