I have RNA-seq studies from two labs that did similar experiments (used same species and both used the same factor with two labels - drug and control). One study had 3 replicates per label (6 samples all together) and other had 4 replicates per label (8 samples all together).
I am wondering if there is a way to compare the results between these two studies?
1) One method may be to compare the DEGs between the two studies. Say the first study had 20 DEGs and second study had 130 DEGs with 8 overlapping between the two studies. Is there a statistical method to test how similar these DEGs are in this situation?
2) Another method is to determine how similar the results from the two studies are not only looking at DEGs, but looking at ALL genes. Possibly determining how similar the FDR values for each and every gene is between the two studies? Maybe some ranking test of FDR values?
My main goal is to determine whether the two studies produced similar results regarding significance. Any advice is greatly appreciated.