I am conducting differential expression analysis in limma for a time course microarray experiment. I have 3 time points (1,2,3) and two conditions (control,disease). My contrast is formulated as:
contrast<-makeContrasts(disease.1-control.1, disease.2-control.2, disease.3-control.3,levels=model)
How can I apply SVA with this experimental setup? Or is there an alternative? The challenge I am facing is SVA seems designed for two class experiments, because the null model requires leaving out the variable of interest, however in this case there isn't one variable but many.