PLINK results interpretation
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
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Have you checked if your dataset contains any missing genotypes?
I agree, you are probably missing some SNP data for those samples.
Yes. you guys are right. There are some samples which contain missing genotypes.
Thank you!