Question: Genomic Inflation Factor Lambda Too Low
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gravatar for mangeles.suarez
5.1 years ago by
mangeles.suarez20 wrote:

I have a bed file with genotype data for around 450000 SNPs and 700 samples. I am performing a logistic regression analysis in PLINK with the option "adjust" to obtain the genomic inflation factor. It gives me a lambda of 1. However I expected a higher value since I have controls from different Spain areas. In fact, if I perform a simple association analysis (--assoc), I obtain a lambda of 1.10. Has anybody an idea of what can cause this difference between the two analysis?

association • 2.9k views
ADD COMMENTlink modified 5.1 years ago by Michael Dondrup46k • written 5.1 years ago by mangeles.suarez20

Inflation factor lambda is too high in GWAS. How to correct this issue (decrease the lambda)? is sort of the exact opposite of this question.

ADD REPLYlink written 5.1 years ago by Michael Dondrup46k

Is it not just a difference between --logistic and --assoc fit?

ADD REPLYlink written 5.1 years ago by zx87547.1k
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