Question: Plink Snp- Quantitative Trait Association - P-Value Is 0
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gravatar for Agatha
5.6 years ago by
Agatha340
Agatha340 wrote:

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 • 2.4k views
ADD COMMENTlink modified 5.6 years ago by Drei50 • written 5.6 years ago by Agatha340
2
gravatar for Drei
5.6 years ago by
Drei50
Melbourne, Australia
Drei50 wrote:

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 COMMENTlink modified 5.6 years ago • written 5.6 years ago by Drei50

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 REPLYlink written 5.6 years ago by Agatha340
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