Hello, I have a question, I know for GWAS, case/control studies use logistic regression, what does it mean when the effect size for a SNP is negative? I'm new to the field so I'd really appreciate it if someone clarified this for me. I've also read that a lot of phenotypes are inverse normally transformed from their raw scores. What does that mean? Thanks!
Assuming that you're talking about the regression coefficients, which are an effect size for logistic regression models, a negative value means the opposite of a positive value. Generally, this would mean that whatever SNP you're looking at is negatively predictive for (i.e. predictive against) the phenotype in question.