[adegenet-forum] SNP alleles

[Jombart, Thibaut]

scale=TRUE will give a lot more weight to rare alleles. So it depends on how much you want to trust these.

I usually go for no scaling (scale=FALSE), so that alleles with low variability are not given an exaggerated weight.

Cheers
Thibaut


________________________________________
From: Andrea Garavito [neagef at gmail.com]
Sent: 17 June 2014 16:24
To: Jombart, Thibaut
Cc: Miguel Navascués; adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] SNP alleles

Thanks Miguel,

You found the problem! I searched and replaced the space characters, redo the analysis et voila! I have my two columns per marker.
With all the reformatting needed to obtain the A/T format from the original excell file, no wonder how those spaces got into the data!

This allows me to rephrase my other question, that got lost in the discussion:

I tried the scale=F and scale=T in the scaleGen function  but I get two radically different results. With scale=T my individuals get separated into only two groups; while with scale=F, individuals get more "harmoniously" distributed over the 2 first PC axis. Which one would be more appropriate according to my data type? Because both seemed in agreement with the origin of individuals, I'm not sure which one represents better the "real picture".

Thank you all for the help

Andrea