Question: SNPTEST v2.5.4 for GWAS analysis
gravatar for Cindy
5 months ago by
Cindy20 wrote:

Hi all,

I am using SNPTEST V2.5.4 to run GWAS analysis. the method newml gives two P values: wald test P and likelihood P, which are different. Which one I should use?

I used Plink to run logistic regression to compare the P values with SNPTEST, the wald-P in PLINK is close to the likelihood P in SNPTEST.

Please help. Appreciate in advance.

snp • 262 views
ADD COMMENTlink written 5 months ago by Cindy20
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