R help - Apr 2011 - hc2Newick is different than th hclust dendrogram

Hi R helpers... I am having troubles because of the discrepancy  
between the dendrogram plotted from hclust and what is wrote in the  
hc2Newick file. I've got a matrix C:
> hc <- hclust(dist(C))
> plot(hc)
with the:
> write(hc2Newick(hc),file='test.newick')
both things draw completely different "trees"...

I have also tried with the raw distance matrix D and also the agnes  
function, but the same happens. The hclus and agnes dendrogram is  
logical, whereas the newick tree is not.

Thanks for any help!
-- 
Jose Sergio Hleap Lozano, M. Sc.
Ph. D. Student, Dalhousie University
Researcher, SQUALUS Foundation

Hi R helpers... I am having troubles because of the discrepancy  
between the dendrogram plotted from hclust and what is wrote in the  
hc2Newick file. I've got a matrix C:
hc <- hclust(dist(C))
plot(hc)
with the:
write(hc2Newick(hc),file='test.newick')
both things draw completely different "trees"...

I have also tried with the raw distance matrix D and also the agnes  
function, but the same happens. The hclus and agnes dendrogram is  
logical, whereas the newick tree is not.

Thanks for any help!

PS> attached C matrix that is a 112x112 matrix
-- 
Jose Sergio Hleap Lozano, M. Sc.
Ph. D. Student, Dalhousie University
Researcher, SQUALUS Foundation

Well, I could not call them "entirely different". See attached
(tree-tv
from TreeView, tree-r from R).
Yes, I had to rotate and mirror the tree in TreeView but that's all.
And yes, I have to ignore the tree length values from the file.
Maybe it is better to post your inquiry to the Bioconductor list (from 
where hc2newick apparently arrives in package 'ctc').
Some humble suggestions:
- don't call a text file .Rdata! Rdata is a specific binary format read 
using load() and saved using save().
- add to the description of your problem how to read the data, i.e.:

z <- scan('data.Rdata')
C <- matrix(z, 112, 112, byrow=TRUE)

- add to your problem description all the packages you loaded to make 
the example work, i.e.:

library('ctc')

Hope it helps
                                     mario

On 04-Apr-11 21:47, Jose Hleap Lozano wrote:
> It was... I have it in my sent box is called data.Rdata...
>
> I am attaching it again!
>
> Thanks
-- 
Ing. Mario Valle
Data Analysis and Visualization Group            | http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 610.82.60
v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91) 610.82.82

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