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help: smartpca plot population shift problem
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2.2 years ago
Zhenyu Zhang • 240
United States

https://github.com/ZhenyuZ/eqtl/blob/master/other/temp.png

Help! I am doing some regular genotype population stratification using smartpca from EIGENSTRAT 5.01. The plot of PC2 ~ PC1 looks like the picture. The color ones are hapmap (blue/lightblue: euro; greenish: asian; redish: blacks; purple: mexican). The grey ones are my samples. There is a shift of coordinates, which indicates something wrong. Does anyone have any idea about the problem?

Details of what I did: I got my sample genotypes, merge with hapmap ones. There are some snp with strand flips, and I have tried both flip or just filter out. Also I have tried to whether remove long-range LD regions; whether to prune local LD SNPs, etc. No matter how I do it, the figure looks like this.

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might be some kind of batch effect in your samples that is driving the PCA

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Could the problem be the hapmap is with grch36, and mine sample with grch37?

I did the merge by their rs names, so I initially thought it's not an issue.

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