I performed an analysis with REGENIE on 2058 patients with a quantitative trait and 7 different covariates. For 5 SNPs I reached a p-value < 5x10-8.
I repeated the linear regression with PLINK and these 5 SNPs are always the top significant, but with a p-value around 1x10-6.
To perform a check, I used another linear phenotype and I performed the GWASes.
P-values from both the two softwares are quite similar (around 1x10-6).
I was wondering the reason of this difference in p-values, if there is any trouble maybe (probably related to the genetic predictors in the Step 1?), and which software I can trust.
Thank you for your kind help and suggestions,
Hi everyone,
I performed an analysis with REGENIE on 2058 patients with a quantitative trait and 7 different covariates. For 5 SNPs I reached a p-value < 5x10-8.
I repeated the linear regression with PLINK and these 5 SNPs are always the top significant, but with a p-value around 1x10-6.
To perform a check, I used another linear phenotype and I performed the GWASes. P-values from both the two softwares are quite similar (around 1x10-6).
I was wondering the reason of this difference in p-values, if there is any trouble maybe (probably related to the genetic predictors in the Step 1?), and which software I can trust. Thank you for your kind help and suggestions,
Best regards, Francesca