Question: High genomic inflation factor and adjusting p values
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gravatar for age00
17 months ago by
age000
age000 wrote:

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?

ADD COMMENTlink modified 17 months ago by olivier.francois30 • written 17 months ago by age000
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gravatar for olivier.francois
17 months ago by
olivier.francois30 wrote:

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.

ADD COMMENTlink written 17 months ago by olivier.francois30
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