I want to know how relevant is it to take control samples when I wish to find only the differentially expressed genes among 3 or more types of cancer. When I go for further analysis like the pathways involved in those cancer from the DE genes or TFs involved, then will not taking control affect it? And what should be the approach to validate some genes from those (as there is no control) in any one of the 3 or more cancers? I am new to microarray..pls help.
If you are just interested in the the differences between different kinds of tumors (basal vs luminal breast tumors) you are fine not including any controls. But when you want to know what differences between the tumor groups are associated with tumor growth/proliferation/development you definitely need to have a non-proliferative control for each tumor group