[adegenet-forum] missing values for global.rtest

[Phil Morin (NOAA Federal)]

Hi,

I've been going through the tutorial for spca analysis in adegenet, and 
ran into an error when I tried to run the global rtest on my data. The 
issue appears to be missing data in my genotypes genind object 
(according to several previous postings). I have found postings that 
simply say "replace NA's", but do not say what to replace them with. It 
runs fine when I replace NA with 0, but it's not clear how that affects 
the results (given that the genotype data are converted to 0, 1, 2 in a 
genind object).

What should NA's be replaced with for the global and local randomized 
tests? Are there other tests that require different types of replacement 
(e.g., mean population value instead of 0)?

-- 
--
Phillip A. Morin, Ph.D.
Southwest Fisheries Science Center
8901 La Jolla Shores Dr.
La Jolla, CA 92037, USA
Phone: 858-546-7165
Fax: 858-546-7003
phillip.morin at noaa.gov
http://swfsc.noaa.gov/mmtd-mmgenetics