Hello, I've ran a genome scan with the software LFMM (frichot et al. 2013) and under all reasonable number of latent factors (k), I get a very high genome inflation factor (2.8-3.3). I'm not sure what could be causing this. If I'm dividing by this high GIF (2.8) and get the expected historgram adjusted p values (http://membres-timc.imag.fr/Olivier.Francois/LEA/files/LEA_1.html), can I trust the results of the genome scan?
The point is we don't know how large GIFs could be in genome scans for selection. I suggest that you increase the number of factors and see if this reduces the GIF. You could also use the newest version of the lfmm program from github https://bcm-uga.github.io/lfmm/index.html. It is much faster that the LEA version, and sometimes better (missing data must be imputed). This could be helpful for checking that your previous discoveries were correct.