Question: How to explain my QQ-plot result
0
gravatar for khlee02
12 weeks ago by
khlee020
khlee020 wrote:

Hello dear,

I am a beginner in exome-seq and have tried to get a threshold of p-value for significant mutations using QQ-plot. However, I couldn't because my QQ-plot looked very weird.

I couldn't figure it out whether it is a something wrong or not, and how I can explain or fix it.

can you help me with this?

Kakao-Talk-20190128-102101242

snp • 291 views
ADD COMMENTlink modified 12 weeks ago by zx87547.1k • written 12 weeks ago by khlee020

Your question lacks any details on what exactly you did what what kind of p-value this is: Brief Reminder On How To Ask A Good Question

ADD REPLYlink written 12 weeks ago by ATpoint15k
1

Are these the results of an association analysis? It seems that your p-values are inflated, which can arise due to different reasons, more commonly due to unaccounted populations structure. There is a lot of literature on interpreting GWAS results. Maybe start with this? https://www.nature.com/articles/nrg1916

ADD REPLYlink written 12 weeks ago by GabrielMontenegro520

I really appreciate your kind comment. I am going to start with it. Is there any good tutorials for basic exome seq?

ADD REPLYlink written 11 weeks ago by khlee020

I am sorry for lack of information. I have done my exome-sequencing in tumor tissue and adjacent normal tissues, and got the p-value from fisher exact test between normal and cancer on each variation. The QQ plot was depicted by qqman in R

ADD REPLYlink written 11 weeks ago by khlee020
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1945 users visited in the last hour