Question: Logistic Regression And Effect Sizes In Gwas
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gravatar for snp_cook12
5.5 years ago by
snp_cook120
United States
snp_cook120 wrote:

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!

gwas snps • 3.9k views
ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by snp_cook120
0
gravatar for Devon Ryan
5.5 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

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.

ADD COMMENTlink written 5.5 years ago by Devon Ryan88k
1

I think a simpler way to say it is that the SNP is protective. Meaning having the SNP is associated with a decrease in the probability of having disease.

ADD REPLYlink written 5.5 years ago by brentp22k
1

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.

ADD REPLYlink written 5.5 years ago by Devon Ryan88k
0
gravatar for snp_cook12
5.5 years ago by
snp_cook120
United States
snp_cook120 wrote:

thank you! that makes sense.

ADD COMMENTlink written 5.5 years ago by snp_cook120
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