Hi all, I have 3 questions regarding genomic inflation factor and how to use it to estimate adjusted p-value. I would appreciate any help. I am running genotype environment association analysis by using latent factor mixed model (LFMM). I am using this to estimate genomic inflation factor:
lambda = median(z.scores^2)/qchisq(1/2, df = 1)
This is a very naive question, please forgive me, but why df should be 1? I thought it should be the number of genetic cluster that I have in my data-set!
Second I am using the lambda value to adjust the P-values:
adjusted.p.values = pchisq(z.score^2/lambda, df = 1, lower = F)
Again here, df should be 1 or it should be the number of population clusters that I have in my data (K = 3)?
By the way, when I estimate lambda according to the above algebra, I am getting low values (0.3-0.4), this means p_values are deflated! What can cause such a Low inflation factors?