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