NA and 0 as a values for beta_SNP

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eliana
Posts: 1
Joined: Tue Mar 08, 2016 9:21 am

NA and 0 as a values for beta_SNP

Postby eliana » Tue Mar 08, 2016 9:43 am

Hello!

i am using PROBABEL to run a GWAS. The output file shows either NaN or 0 as a Beta values. In a previous forum, this issue was presented for a few SNPs and running a regression in R was suggested. However, I am having the problem for all SNPs. What could be wrong and how I could fix it?. Many thanks in advance

Best,

Eliana
Last edited by lckarssen on Tue Mar 08, 2016 9:50 am, edited 1 time in total.
Reason: Fixed minor spelling error

lckarssen
Site Admin
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Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: NA and 0 as a values for beta_SNP

Postby lckarssen » Tue Mar 08, 2016 9:52 am

What kind of regression are you running? Linear, logistic or CoxPH?
What version of ProbABEL do you use?

Could it be that all your SNPs are rare/have a very low MAF? Please also check the imputation Rsq (both can be found in the info file).
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Lennart Karssen
PolyOmica
The Netherlands
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