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hakyim / TO-DELETE-PrediXcan

Code for the in-dev PrediXcan Project
MIT License
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Does the genotype build make a difference on prediction?? #27

Closed gpwhiz closed 6 years ago

gpwhiz commented 6 years ago

Hello, I wanted to know if the genotype build makes any difference on the gene expression prediction. My genotype data is on hg18, and I am using GTEx v7 as reference in PrediXcan. Do I need to convert to hg19, then Gh38, and then do the prediction? Will that improve the accuracy of prediction ?? I have already done prediction using hg18 genotypes without any errors. Please advise.

hakyim commented 6 years ago

Hi

the models in V7 were trained with hg19 so it will work best with that build. Our models should be robust to using other builds since we are matching rsids but of course there will be some corner cases where hg19 will do much better.

I hope this helps Haky

On Mon, Apr 9, 2018 at 7:33 PM, gpwhiz notifications@github.com wrote:

Hello, I wanted to know if the genotype build makes any difference on the gene expression prediction. My genotype data is on hg18, and I am using GTEx v7 as reference in PrediXcan. Do I need to convert to hg19, then Gh38, and then do the prediction? Will that improve the accuracy of prediction ?? I have already done prediction using hg18 genotypes without any errors. Please advise.

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