I was analyzing dataset consists of both cancer cell lines and tissue samples. Do I need to find DEGs separately or need to combine? Any difference between genes expressed in cell lines and tissue samples?
I think you're a bit off on your understanding of differential expression analysis, I'd read through the Limma users guide to get an idea of how you'd go about analysing microarray data in this way. I'd avoid combining different datasets, as that requires a lot of knowledge on the subject, and often just isn't feasible.
