I have a microarray experiment (GSE63706) with 6 time points, tissues, three species and two replication. i am going retrieve genes with fold change more than two.
may someone tell me a design for limma because i got confused as already..
I have a design for treatment and normal in fout time points but i can adapt for my case
the design is like below
X <- ns(targets$time.h, df= 2)
Group <- factor(targets$treatment)
design <- model.matrix(~Group*X)
colnames(design) <- c("Intercept", "Groupheat","Control_X1", "Control_X2","Heated_X1", "Heated_X2")
fit <- lmFit(data, design)
fit <- eBayes(fit)