This is a very general question about an analysis I have been trying to do for quite sometime, but I still do not know how to proceed. I have a series of experiments performed on a single organism which include experiments like: comparing antibiotic sensitive and antibiotic resistant strains, comparing different motility adaptations, comparing stress related adaptations. However, I want to find a set of genes that are commonly dysregulated in all these experiments. I am not sure that how would I find commonly dysregulated genes in these different experiments. I could either just compare the DE genes obtained in each expe and find common or I could use the count files of these experiments together in a single DDS object. And even if I do use their counts together in a single DDS object, how would I normalize them.
Any help would be highly appreciated.