PLINK results interpretation
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7.4 years ago
genetic ▴ 40

I found some issues in results of PLINK software.

Let's say, we have 145 cases and 828 controls.

I got below table using --model and --fisher.

However, I do not understand why some individuals do not included in AFF and UNAFF columns.

For example, for SNP 17:74017478, 2+139=141 (I think it should be 145, but not sure why 4 individuals are excluded).

Does anyone can help me to understand why I got 141 instead of 145?

SNP          P-value   F_A       F_U       AFF    UNAFF
2:179702437  3.03E-01  0.01379   0.00786   4/141  13/814
6:155750075  3.84E-01  0.003448  0.001208  1/144  2/826
17:74017478  4.46E-06  0.007092  0.06471   2/139  106/713
SNP software-error • 1.7k views
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4
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Have you checked if your dataset contains any missing genotypes?

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1
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I agree, you are probably missing some SNP data for those samples.

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1
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Yes. you guys are right. There are some samples which contain missing genotypes.

Thank you!

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