Logistic regression with PLINK, p-values

Question

[monsegd14]

We want to evaluate the association of several SNPs in an population with a disease. After the bech work we have a database with the results. We use the software PLINK to run logistic regression analysis including covariates like the sex of the patientcs. The output file give me several p-values :

My questions is: Which p-value give me the association between the SNP and the disease? which p-value reflect the effect of the covariate?

[Devon Ryan]

You'll need to either upload an image of that table somewhere or simply make a table in your post and manually type in the values.

[monsegd14]

The output file is:

SNP     Allele     Test       OR      SE      L95     U95     P
1       c          ADD        0.2     0.3     0.1     0.3     3.728e-05
1       t          ADD        4.9     0.3     2.8     8.8     3.728e-05
1       C          SEX        1.5     0.3     0.7     3.2     0.325
1       T          SEX        1.8     0.6     0.4     7.1     0.382
1       C          ADDxSEX    1.1     0.4     0.4     2.5     0.825
1       T          ADDxSEX    0.9     0.4     0.3     2.2     0.825

[monsegd14]

Thank you so much for your help. I was totally lost with this kind of analysis because I thought that the ADD p-value was for SNP-disease interaction (the p-value is significant) and SEX p-value for Sex-disease association (not significant) but I do not understad the ADDxSEX colum (not significant and higher tan SEX-p-value) I mean with a P-value so high does it mean that SEX has influenced in the disease?? (because when SEX effect is added, the p-value change from significant to not significant)

I am totally lost

[Devon Ryan]

Gender has an insignificant p-value, so no, it doesn't seem to influence anything here. "ADDxSEX" is looking at a possible interaction between the disease and gender, for which there also appears to be none. You might want to have a local statistician walk you through what a logistic regression is and what an interaction means.

[monsegd14]

Thank you son much again...but the relation between the SNPs-disease corrected by sex, which analyse or p-value is??

Sorry for my ignorance, and thank you for your time and your help

[Devon Ryan]

ADD is the SNP disease result while accounting for gender.

Answer 1

[chrchang523]

In your output file, ADD p-values are for SNP-disease association, SEX p-values are for sex-disease association, and ADDxSEX is for the multiplicative interaction term.

[monsegd14]

Thank you!!!!!

I want to apply the same analyse with the age of the patients, but I have problems to upload age in plink. I have tried to code the age: 0 if the age is <60 and 1 if the age is >60

Thank you!!!!