Plink Snp- Quantitative Trait Association - P-Value Is 0
1
0
Entering edit mode
7.9 years ago
Agatha ▴ 350

I have run PLINK --assoc for a list of snps and the associated genotypes and qt measurements.

The SNP I have added as control (control= it is known that it is highly associated with the analyzed quantitative trait ) is returned as having a p-value of 0. When doing a separate linear regression analysis in R the p-value is 1.212e-308 .

The genotypes have been used for already published studies.

The p-value is normally very low for that association, but why is it returned as 0 by plink?

Plink returned the 3 expected most significant SNPs (out of 700) as having a p-value of 0.

plink • 3.5k views
ADD COMMENT
2
Entering edit mode
7.9 years ago
Drei ▴ 50

1.212e-308 is extremely low - I'd imagine PLINK rounds off any P-value low enough to 0. Just how low isn't in the documentation, but if you need to know, I suggest generating some fake data that would give you a range of low p-value and feeding it all to PLINK to see at which point it turns a tiny p-value into 0. Which might be pretty difficult, actually.

ADD COMMENT
0
Entering edit mode

That must be the case ... I have looked in the documentation, forums, examples but I couldn't find anything similar to what I have or any information about the thresholds...

ADD REPLY

Login before adding your answer.

Traffic: 2241 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6