(1) To make the method more robust to outliers in the phenotype data, FastQTL has an option that allows to quantile normalize the phenotype quantifications prior to any analysis. This ensures that phenotype quantifications are normally distributed with mean 0 and standard deviation 1. Quantile normalization is implemented as in the R/rntransform function of the GenABEL package (Aulchenko et al., 2007).
