I am performing a quantitative trait association between the expression of one gene and ~400,000 methylation values. First, both variables are rank inverse normal transformed, adjusted for confounders (technical and for family structure) in a mixed-effects model and we use the residuals for the association. Then we do a linear regression between the residuals of expression and each methylation site, adding other four confounders in the model (age, BMI, etc.). The sample size is of ~500. For the association we are using MatrixEQTL.
When we check the p-values, they are clearly inflated. Is it something that I have to be concerned about? Did I probably miss something in the analysis? Thanks in advance.