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!
2 answers
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.
I actually used the "protective" nomenclature at first and then changed it. In reality, I don't think it's proper to call a SNP itself protective unless you then show with other experiments that it's not just simply associated with other changes that are actually the ones conveying the protective effect.
thank you! that makes sense.
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