Hello, I have microsatellite data and I would like to analyze them using PCoA in R. I would like to use following genetic distance: Goldstein's (1995) (dμ)2 and Nei's chord distance (1983). I calculated those distances in MSA (Dieringer and Schlötterer 2003), because I didn't find any possibility to calculate them in R. I imported the distances like that: dist.dms <- read.csv("dms_ind.txt", header=TRUE, sep="\t", dec=".", row.names=1) dioszegia.dist.dms <- as.dist(dioszegia.dist.dms) class(dioszegia.dist.dms) [1] "dist“ dms_ind.txt is ordinary square matrix with diagonal. But using of dudi.pco() from ade4 package fails: pcoa <- dudi.pco(dist.dms, scannf=FALSE, nf=3) Warning message: In dudi.pco(dioszegia.dist.dms, scannf = FALSE, nf = 3) : Non euclidean distance When using Euclidean distance (function dist()), it works fine. It produces some results despite the above error, but the results are very far from those I get using dist() function. And the results don't look realistic. What do I do wrong? :-) Have a nice day! Vojtěch
-- Vojtěch Zeisek Komunita openSUSE GNU/Linuxu Community of the openSUSE GNU/Linux http://www.opensuse.org/ http://trapa.cz/
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