Question: PLINK results interpretation
0
gravatar for genetic
3.8 years ago by
genetic40
United States
genetic40 wrote:

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

Thanks,

 

       

 

 

 

 

 

 

 

snp software error • 920 views
ADD COMMENTlink written 3.8 years ago by genetic40
4

Have you checked if your dataset contains any missing genotypes?

ADD REPLYlink written 3.8 years ago by chrchang5234.9k
1

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

ADD REPLYlink written 3.8 years ago by QVINTVS_FABIVS_MAXIMVS2.2k
1

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

Thank you!

ADD REPLYlink written 3.8 years ago by genetic40
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