I have a data set of two different cell lines compositions for a developmental assay in Drosophila. By itself it wouldn't be so difficult to analyze it, but the problem is in the composition of each of the cell lines.
The first cell line has four different subtypes (A,B,C,D) the second one has only subtype C. It is expected to have subtle changes for some of the genes, but we're not really sure how many and what kind of changes.
I was wondering if this can be analyzed in a straight forward way. What can I say about genes differences between these two populations?
Is it possible to compare them in the standard way, just compare one to the other?
I am not sure it would tell me anything significant. If a genes is DE in the first population, what does it means?
If anyone know of a source or reference of some kind for this kind of experiment, I would appreciate a hint.