I am working on an eQTL project. I run the eQTL identification using MatrixEQTL. After I get the results from the function of Matrix_eQTL_main, I just run a QQ-plot. Here is the output figure:
I performed a variance-stabilizing transformation on the gene expression data. Does the result show inflation? As I learned from the manual page on MatrixEQTL (http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/R.html#cis), their -log10(pvalue) is around 0-10. But my range for -log10(pvalue) is much greater than that. They did show some overlaps from 0-1. So I want to know if the result is inflated.
Many thanks in advance.