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


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

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?

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
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