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
NA and 0 as a values for beta_SNP
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NA and 0 as a values for beta_SNP
Last edited by lckarssen on Tue Mar 08, 2016 9:50 am, edited 1 time in total.
Reason: Fixed minor spelling error
Reason: Fixed minor spelling error
Re: NA and 0 as a values for beta_SNP
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).
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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Lennart Karssen
PolyOmica
The Netherlands
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