Question: Significance of PLINK epistasis p-values
gravatar for viavialin
6.2 years ago by
viavialin70 wrote:

I performed an epistasis analysis on PLINK using the following options-



--epi1 1


The output from PLINK reports tests significant at a p-value (asymptotic p-value) <1e-4 by default. Since I am not performing a GWAS and I only have 400 SNPs, I changed the output to include all tests.


Do I therefore consider all interaction tests smaller than p<1e-4 as significant or stick to the 'usual' p<0.05?


I performed a Bonferroni correction and nothing was significant. Therefore I am confused on how to interpret the PLINK output p-values.


p-values plink epistasis • 2.8k views
ADD COMMENTlink modified 5.0 years ago by Biostar ♦♦ 20 • written 6.2 years ago by viavialin70

You should read up on I would NOT go with the p<0.05 cutoff. Bonferroni correction might be a bit too conservative. Anything significant if you check FDR? If not, you might be out of luck. 

ADD REPLYlink written 6.2 years ago by bdeonovic180

try LAMP algorithm or lamplink tool directly;

ADD REPLYlink written 4.3 years ago by Rm8.0k
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