Question: When will QQplot be inflated? (inflated qqplot generated from GWAS logistic regression using PLINK)
gravatar for zzy
2.7 years ago by
zzy10 wrote:

Hi, everyone,

I have been doing GWAS on a scaled phenotype (from 0 to 16, where 0 represents extremely good, and 16 represents extremely bad). Also I have two covariates. Since scaled phenotype is not normally distributed, I binarized it into 0 and 1, and tried logistic regression with or without covariates using PLINK (v 1.9). I am quite confused about the --genotypic and --interaction parameters from PLINK though I had already read the PLINK manual. Logistic regression would give totally different results (p values of ADD or GENO_2DF) concerning these two parameters, and I also got inflated qqplots which squeezed the diagonal line almost horizontal. This inflated qqplot mainly occurred when I included --genotypic parameter into logistic regression, and I want to know why did this happen.


ADD COMMENTlink written 2.7 years ago by zzy10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 742 users visited in the last hour