Using MatrixEQTL R package, I am performing both cis and trans eQTL analyses in order to find some SNPs associated with two genes of interest (for which we have profiled two specific genes of interest using qRT-PCR). As a result, interestingly, whereas there were NO significant cis-eQTLs for both genes, there were many trans-eQTLs of significance (FDR<0.05).
I tried to look into the detailed data distribution, and realized the distribution is like the below attached picture. Given that there were only two subjects (among 94 subjects) that have ALT/ALT, I am wondering if the result from this analysis is still valid or not...
Please advise me.