From: Jeffrey DaCosta <dacostaj_at_unlv.nevada.edu>

Date: Fri 13 May 2005 - 05:36:03 EST

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Fri May 13 05:33:24 2005

Date: Fri 13 May 2005 - 05:36:03 EST

I want to create a MDS plot with pairwise Fst values derived from a
population genetics project. My Fst values are in a tab-delimited file
(lower triangle only) that I view with Excel. When I use the cmdscale
command I get the message:

Error in cmdscale(x) : Distances must be result of dist or a square
matrix

In addition: Warning messages:

1: "^" not meaningful for factors in: Ops.factor(left, right) 2: "^" not meaningful for factors in: Ops.factor(left, right) 3: "^" not meaningful for factors in: Ops.factor(left, right) 4: "^" not meaningful for factors in: Ops.factor(left, right)

I transformed my values using the dist command, but the resulting plot is not right.

My file of Fst values are the estimates of distance that I want to
directly use in the MDS analysis. Looking for help in making my Fst
file read in R as a distance matrix for this to work.
-Jeff DaCosta

dacostaj@unlv.nevada.edu

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Fri May 13 05:33:24 2005

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