On Wed, 2004-09-08 at 21:31, Doran, Harold wrote: > Thank you. Quick clarification. isoMDS only works with dissimilarities. > Converting my similarity matrix into the dissimilarity matrix is done as > (from an email I found on the archives) > > > d<- max(tt)-tt > > Where tt is the similarity matrix. With this, I tried isoMDS as follows: > > > tt.mds<-isoMDS(d) > > and I get the following error message. > > Error in isoMDS(d) : An initial configuration must be supplied with > NA/Infs in d. I was a little confused on exactly how to specify this > initial config. So, from here I ran cmdscale on d as > This error message is quite informative: you have either missing or non-finite entries in your data. The only surprising thing here is that cmdscale works: it should fail, too. Are you sure that you haven't done anything with your data matrix in between, like changed it from matrix to a dist object? If the Inf/NaN/NA values are on the diagonal, they will magically disappear with as.dist. Anyway, if you're able to get a metric scaling result, you can manually feed that into isoMDS for the initial configuration, and avoid the check. See ?isoMDS.
> > d.mds<-cmdscale(d) > > which seemed to work fine and produce reasonable results. I was able to > take the coordinates and run them through a k-means cluster and the > results seemed to correctly match the grouping structure I created for > this sample analysis. > > Cmdscale is for metric scaling, but it seemed to produce the results > correctly. > > So, did I correctly convert the similarity matrix to the dissimilarity > matrix? Second, should I have used cmdscale rather than isoMDS as I have > done? Or, is there a way to specify the initial configuration that I > have not done correctly. If you don't know whether you should use isoMDS or cmdscale, you probably should use cmdscale. If you know, things are different. Probably isoMDS gives you `better'(TM) results, but it is more complicated to handle. cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland Ph. +358 8 5531526, cell +358 40 5136529, fax +358 8 5531061 email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa/ ______________________________________________ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
