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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