Hi, I feel confused when i calculate odd ratio of per snp by plink. My problem is described as followings:
when i run this command plink --noweb --bfile mydata --assoc ,I get this results:
CHR SNP BP A1 F_A F_U A2 CHISQ P OR
1 rs3094315 792429 G 0.1489 0.08537 A 1.684 0.1944 1.875
1 rs4040617 819185 G 0.1354 0.08537 A 1.111 0.2919 1.678
1 rs4075116 1043552 C 0.04167 0.07317 T 0.8278 0.3629 0.5507
1 rs9442385 1137258 T 0.3723 0.4268 G 0.5428 0.4613 0.7966
1 rs11260562 1205233 A 0.02174 0.03659 G 0.3424 0.5585 0.5852
when I use another command plink --noweb --bfile mydata --logistic, I get this results:
CHR SNP BP A1 TEST NMISS OR STAT P
1 rs3094315 792429 G ADD 88 2.061 1.381 0.1672
1 rs4040617 819185 G ADD 89 1.804 1.12 0.2629
1 rs4075116 1043552 C ADD 89 0.5303 -0.9272 0.3538
1 rs9442385 1137258 T ADD 88 0.8197 -0.687 0.4921
1 rs11260562 1205233 A ADD 87 0.5758 -0.5877 0.5567
So, why is odd ratio of the same snp different?
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written
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dandanli0365 •
Basically they use different methods for the calculation of the odds ratio - logistic uses the logistic regression model and assoc uses allele counts. Your differences aren't that large but the rarer the allele the greater the difference you may see. Have a read of Plink 1.07 manual - it is outlined in this page.
thank you very much! now, i still feel a little confused. I know how to calculate OR in '-assoc'. I wonder how to calculate in logistic regression. Here is my guess: coefficient is firstly calculated in logistic regression and then the exponent of the coefficient is used for OR. Is it right?
In the interest of learning you can test your theory by implementing the --beta flag into your analysis. This will return the regression coefficients. plink --bfile mydata --logistic --beta
I have tried it and knew it well, thank you very much again!
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