Genomic Inflation Factor Lambda Too Low

0

Entering edit mode

10.7 years ago

mangeles.suarez ▴ 20

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 • 5.4k views

ADD COMMENT • link updated 10.7 years ago by Michael 55k • written 10.7 years ago by mangeles.suarez ▴ 20

0

Entering edit mode

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 REPLY • link 10.7 years ago by Michael 55k

0

Entering edit mode

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

ADD REPLY • link 10.7 years ago by zx8754 12k

Login before adding your answer.