I have more of a philosophical question. I've seen papers which use skepticism in interpreting trans-eQTLs due to alignment errors or batch effects. I am doing an analysis currently with RNA-seq and genotype data, trying to find significant eQTLs.
So far I've found a lot of trans-eQTLs above the statistical significance threshold (FDR = 0.05; p = 1e-3) and zero to very minimal number of cis-eQTLs. During literature survey I found quite the opposite where people tend to find a lot of cis-eQTLs and less trans-eQTLs (which makes sense due to LD and other factors).
So my question is what caution should I exercise in interpreting this event of observing abundantly more trans-eQTLs than their cis counterparts (or is this common). Any comments/discussion on this matter would greatly help my understanding of interpreting eQTLs as winner's curse is a very common phenomenon.