[R] which function to use to do classification

[Adaikalavan Ramasamy]

I find it helpful to explain to my colleagues from non-mathematical
background that in classification the classes are predefined and in
clustering the classes (and sometimes the number of classes) are not.

I prefer the use of the term "class discovery" over clustering when
people try to cluster samples in order to derive meaningful classes.

Regards, Adai



On Wed, 2006-03-29 at 18:52 -0500, Liaw, Andy wrote:
> In addition to Brian's comment, Gordon's book, already in 2nd edition, is
> all about clustering, but the title is simply `Classification'.
> 
> Andy
> 
> From: Sean Davis
> > 
> > We have to be careful here.  Classification (which is the 
> > terminology that the original poster used) is NOT the same as 
> > clustering, although the two are often confused.  If the 
> > original poster wants to do clustering and examine the 
> > results for the presence of three clusters, that is fine and 
> > there are many methods for clustering that could be used.  
> > However, classification will require a different set of 
> > tools.  If the clustering tools already pointed out are not 
> > doing what is needed (that is, that Cao actually is 
> > interested in clustering and not classification), then 
> > perhaps a further explanation of what the problem would help clarify.
> > 
> > Sean
> > 
> > 
> > On 3/29/06 1:46 AM, "Jacques VESLOT" <jacques.veslot at cirad.fr> wrote:
> > 
> > > try this (suppose mat is your matrix):
> > > 
> > > hc <- hclust(dist(mat,"manhattan"), "ward")
> > > plot(hc, hang=-1)
> > > (x <- identify(hc)) # rightclick to stop
> > > cutree(hc, 3)
> > > 
> > > km<- kmeans(mat, 3)
> > > km$cluster
> > > km$centers
> > > 
> > > pam(daisy(mat, metric = "manhattan"), k=3, diss=T)$clust
> > > 
> > > 
> > > 
> > > Baoqiang Cao a écrit :
> > > 
> > >> Thanks!
> > >> I tried kmeans, the results is not very positive. Anyway, thanks 
> > >> Jacques! Please let me know if you have any other thoughts!
> > >> 
> > >> Best regards, 
> > >>    Baoqiang Cao
> > >> 
> > >> ======= At 2006-03-29, 00:08:44 you wrote: =======
> > >> 
> > >>  
> > >> 
> > >>> if you want to classify rows or columns, read:
> > >>> ?hclust
> > >>> ?kmeans
> > >>> library(cluster)
> > >>> ?pam
> > >>> 
> > >>> 
> > >>> Baoqiang Cao a écrit :
> > >>> 
> > >>>    
> > >>> 
> > >>>> Dear All,
> > >>>> 
> > >>>> I have a data, suppose it is an N*M matrix data. All I 
> > want is to 
> > >>>> classify it into, let see, 3 classes. Which method(s) do 
> > you think 
> > >>>> is(are) appropriate for this purpose? Any reference will be 
> > >>>> welcome! Thanks!
> > >>>> 
> > >>>> Best,
> > >>>> Baoqiang Cao
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>> 
> > -------------------------------------------------------------------
> > >>>> -----
> > >>>> 
> > >>>> ______________________________________________
> > >>>> R-help at 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
> > >>>> 
> > >>>>      
> > >>>> 
> > >>> .
> > >>>    
> > >>> 
> > >> 
> > >> = = = = = = = = = = = = = = = = = = = =
> > >> 
> > >> Baoqiang Cao
> > >> caobg at email.uc.edu
> > >> 2006-03-29
> > >> 
> > >> 
> > >>  
> > >> 
> > > 
> > > ______________________________________________
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> > > PLEASE do read the posting guide! 
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> > 
> > ______________________________________________
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> > 
> >
> 
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