I started using LIMMA for checking differential expression of genes in control and stress treatments (2 replicates for each condition). I constructed a design matrix where replicates for each one goes to the same group like group1 contains rep1 and rep2 for control and group2 contains rep1 and rep2 for stress treatment. Next, I build a contrast matrix comparing group2 with group1. Finally, I got the results from LIMMA that gives me the fold change values.
My question is how do I know that LIMMA is looking for fold change of control over stress or stress over control? In other words, how to decide whether the genes with more positive log2 fold change values are more highly expressed (overexpressed) in the stress condition or in the control condition.
Hope my query is understandable and any help would be very much appreciated.
Many thanks, RT