Bad Manhattan Plot

[happy]

What might be wrong with these Manhattan Plots obtained from MLM and GLM??

Genotype file, phenotype file, Q value of Sturcutre (K) are all the same.

Can someone familiar with these explain?

(1) Manhattan Plot from MLM:

(2) Manhattan Plot from GLM:

[Terry Casstevens]

Which version of TASSEL?  This looks like an old version.  I would recommend updating to the latest build.

Best,

Terry

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[happy]

Terry I am currently using TASSEL version 5.2.31. What is the latest version?

On Tuesday, May 16, 2017 at 12:35:31 PM UTC+8, Terry wrote:

Which version of TASSEL?  This looks like an old version.  I would recommend updating to the latest build.

Best,

Terry

On Sun, May 14, 2017 at 9:01 PM, happy <cbr...@gmail.com> wrote:

What might be wrong with these Manhattan Plots obtained from MLM and GLM??

Genotype file, phenotype file, Q value of Sturcutre (K) are all the same.

Can someone familiar with these explain?

(1) Manhattan Plot from MLM:

(2) Manhattan Plot from GLM:

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[Peter Bradbury]

Could you be specific about what you think is wrong with the Manhattan plots? Ugly colors? If the you are referring to the difference between the results for MLM and GLM, then yes, that is very unusual. In particular, the p-values for MLM are generally smaller than they are of GLM. I suspect it is something related to your particular data. Without looking at the data it is difficult to diagnose. One thing to check would be to see if you have any extreme outliers in the phenotype.

Peter

[Aleyda Sierra]

Hi Happy, did you manage to solve the issue? Because Im on the same situation.

Cheers:) 

[Aleyda Sierra]

Hi Peter,

Im also getting those small p values, I was thinking that it has something to do with the structure of the population because when I run the GLM everything goes well. I tried before using the command line (MLM) and everything ran okay so any idea of what I could be doing wrong?

In advance, thank you!

[happy]

Yes Aleyda Sierra,

The solution lies in your structure (Q matrix) data file. Remove 1 Q from your Q data so that the software can statistically calculate the linear relations.

Take for example if you Q = 3, then you must remove 1 Q  collum from your data file. Your new Q = 3 file will now only have 2 Q value columns in the data file.

I trust it will definitely work.

All the best