Epistasis Analysis PLINK2

Hello, I run an epistasis analysis with PLINK with a small sample 25 cases and 31 controls using 20K non in LD. I obtained more than 2000 P values = 0. I can't figure out why. Anyone encountered this before? Thanks S.

snp

• 2,095 views • link

updated 10.2 years ago by Biostar

• written 10.2 years ago by cge •

0 answers

No answers yet.

More posts like this

How to merge 20K single-sample VCFs *without* using plink or plink2?
written 4.2 years ago by kynnjo •

I have ~20K single-sample VCFs, all covering the same sites, that I want to merge into a single ~20K-sample VCF. In the past, I have …
plink
written 4.4 years ago by ooo •

Hi all, I use plink for gene association test. command : plink --file myplink --noweb --allow-no-sex --geno 0.05 --mind 1 --hwe 0.001 --out cleaned log …
How to generate haplotypes with SNPs from WGS ?
written 5.4 years ago by gigotdagneau •

Hi, I have a .vcf file with 150 000 SNPs on the X chromosome and genotypes for 5 samples from WGS. I tried using plink. …
What is the smallest number of cases you can have in a GWAS before interpretation starts becoming t…
written 5.7 years ago by curious

Lets say you had 100,000 samples, but were looking at some super rare diseases. At some point I would think even given the huge overall …
Epistatic effect for two alleles
written 6.9 years ago by khn

Hello, I want to check the epistatic effects for two alleles that are significantly associated with a phenotype. Cases and controls are both about 30 …
GWAS missing p-values
written 7.5 years ago by emmacomp •

Hello, when running a logistic regression on 250 cases and 2000 controls, the resulting GWAS has completely missing p-values in the middle. I have attached …
Inflated qq plot and genomic inflation est. lambda
written 8.2 years ago by khn

Hello, I have merged two datasets from different platforms after imputation (Dataset1 includes 20 cases and 2000 controls, and about 450000 SNPs per chromosome. Dataset2 …
association analysis with stratification
written 9.1 years ago by alessandrotestori7

Hello! I want to run a classical genome-wide association analysis (cases vs controls) in order to understand whether particular polymorphisms are relevant in a disease. …
Error in quantro function
written 10.7 years ago by cge •

Hi, I am using the function "quantro" (library R-quantro) to test the distribution of beta values among cases and controls to assess if it is …
Why Plink stoped analyzing without make a new PED file and MAP file?
written 10.8 years ago by Bahar •

Hello friends I ran following command in plink but my plink suddenly crashed and stop the analysis, although, I ran this command for several times …