We treat tumor cells with compound A, compound B, compound A + B mixed, and compound A-B linked respectively with different concentrations of compound(s) for each group, and we have controls (total 5 groups). We measure the gene expression for each group.
One of our goals is to find out if A-B linked & A + B mixed causes differential gene expression. If yes, what the genes are. A-B linked meaning A & B are linked together chemically and become a new compound.
A straightforward comparison is just to compare A-B linked with A + B mixed (a nested question: do a linear regression of gene expression level ~ compound concentration and compare the beta's? DESeq or edgeR might not be appropriate I am afraid). But we have experimental data for the other three groups (control, A, B). Can we make use of such datasets as well?
