Displaying 20 results from an estimated 10000 matches similar to: "Ward clustering problem"
2008 Mar 08
1
Elbow criterion plots for determining k in hierarchical clustering
Hi There,
I'm working on some cluster analyses on a large data-set using hclust with
Wards method and Manhattan (city block) distance measures. I've created
dendrograms to illustrate the clustering criteria, but would like to create
a plot to examine for the classic elbow criterion to use in determining the
best number of clusters. Ideally I'd like to plot percent variance
explained
2002 Jul 18
0
Plotting Clustering Groups Separately
Hi
As a beginer with R I have been trying to plot dendrograms for individual
groups after using cutree.
The example in the help files appears to work fine for Euclidean distances
using the "average" clustering method. However, when I use the "Ward" method
the the reprocessed subgroup does not appear to have the same structure as
it did when the whole dataset was processed.
Is
2004 Jun 17
1
Re: Clustering in R
Thanks a lot, Michael!
I cc to R-help, where this question really belongs {as the
'Subject' suggests itself...} -- please drop 'bioconductor' from
CC'ing further replies.
>>>>> "michael" == michael watson (IAH-C) <michael.watson at bbsrc.ac.uk>
>>>>> on Thu, 17 Jun 2004 09:16:59 +0100 writes:
michael> OK, admittedly it
2014 Jul 25
0
clustering with hclust
Hi everybody, I have a problem with a cluster analysis.
I am trying to use hclust, method=ward.
The Ward method works with SQUARED Euclidean distances.
Hclust demands "a dissimilarity structure as produced by dist".
Yet, dist does not seem to produce a table of squared euclidean distances,
starting from cosines.
In fact, computing manually the squared euclidean distances from cosines
2011 Mar 02
2
clustering problem
Hi,
I have a gene expression experiment with 20 samples and 25000 genes each.
I'd like to perform clustering on these. It turned out to become much faster
when I transform the underlying matrix with t(matrix). Unfortunately then
I'm not anymore able to use cutree to access individual clusters. In general
I do something like this:
hc <- hclust(dist(USArrests), "ave")
2007 Nov 27
2
exporting clustering results to table
Hello list,
the following approach did not work:
clustersA <- pam(distances, nkA, diss=TRUE);
gc();
filenameclu = paste("filenameclu", ".txt");
write.table(clustersA , file=filenameclu,sep=",");
although it worked with
clustersA <- hclust(distances, method="ward");
and a consecutive
kclassA <- cutree(clustersA, k=nkA);
filename =
2012 Aug 12
0
Different cluster orderings from cutree() and cut.dendrogram()
Hi!
I just discovered that cutree() and cut.dendrogram() do not assign the
same cluster numberings when called on the same tree. More specifically,
cutree() assigns cluster numbers by order of appearance in the data,
while cut.dendrogram() sorts clusters by height (see example below). I
guess this is for historical reasons?
I'm hit by this difference when I want to get a vector of cluster
2003 Dec 11
1
cutree with agnes
Hi,
this is rather a (presumed) bug report than a question because I can solve
my personal statistical problem by working with hclust instead of agnes.
I have done a complete linkage clustering on a dist object dm with 30
objects with agnes (R 1.8.0 on
RedHat) and I want to obtain the partition that results from a cut at
height=0.4.
I run
> cl1a <- agnes(dm, method="complete")
2003 Dec 11
1
cutree with agnes
Hi,
this is rather a (presumed) bug report than a question because I can solve
my personal statistical problem by working with hclust instead of agnes.
I have done a complete linkage clustering on a dist object dm with 30
objects with agnes (R 1.8.0 on
RedHat) and I want to obtain the partition that results from a cut at
height=0.4.
I run
> cl1a <- agnes(dm, method="complete")
2010 Jun 23
1
Clustering
Hi,
I use the following clustering methods and get the
corresponding dendrograms for single, complete, average, ward and
kmeans clustering.
This gives the dendrograms, but doesn't show the calculation-way.
My question: is there a possibility to show this calculation steps
(cluster steps) in matrix or graphical form?
Mit freundlichen Gr??en
Ralph Modjesch
2012 Feb 23
2
Advice on exploration of sub-clusters in hierarchical dendrogram
Dear R user,
I am a biochemist/bioinformatician, at the moment working on protein
clusterings by conformation similarity.
I only started seriously working with R about a couple of months ago.
I have been able so far to read my way through tutorials and set-up my
hierarchical clusterings. My problem is that I cannot find a way to obtain
information on the rooting of specific nodes, i.e. of
2011 Dec 12
1
Is there a way to print branch distances for hclust function?
The R function hclust is used to do cluster analysis, but based on R
help I see no way to print the actual fusion distances (that is, the
vertical distances for each connected branch pairs seen in the cluster
dendrogram).
Any ideas? I'd like to use them test for significant differences from
the mean fusion distance (i.e. The Best Cut Test).
To perform a cluster analysis I'm using:
x
2006 Mar 23
0
kmeans Clustering
Dear WizaRds,
My goal is to program the VS-KM algorithm by Brusco and Cradit 01 and I have
come to a complete stop in my efforts. Maybe anybody is willing to follow my
thoughts and offer some help.
In a first step, I want to use a single variable for the partitioning process.
As the center-matrix I use the objects that belong to the cluster I found with
the hierarchial Ward algorithm. Then,
2000 Dec 05
0
calculation of inertial difference with huygens theorem in ward clustering ?
Hello to the R people,
within ward clustering the distance calculated to decide the clustering
of 2 subsets (h1 and h2) is the variation of inertia :
d(h1,h2)=I(h1Uh2)-I(h1)-I(h2);
i've been said that a way to calculate faster this d(h1,h2) is using the
huygens theorem decomposing the inertia into "the inertia to the
centroid + the distance to an axe" (that's my version ...). My
2004 Jul 21
2
Cutting heatmap dendrogram
Hello,
I've been clustering my data using hclust and cutting the resulting tree
with cutree. Separately, I visualize the clusterings with heatmap. Is it
possible to have the dendrogram on the heatmap reflect the cutree results?
That is, instead of having one large dendrogram, it would have 4 or 25 in
the example below. Any guidance on if that's possible or not, and what
kinds of
2012 Dec 06
1
tool for cluster analysis
I have Windows XP Professional Version 2002 and the R-Version 2.1.1.
I did cluster analysis with the cluster package and the agnes (method =
?ward?).
The results are satisfactory.
But the dendrogram of agnes is confused to work with the results.
Is there a tool, I can get a clear arrangement of the results for the
cluster analysis.
For example a matrix with different numbers for each group.
2000 Nov 16
0
RNN Algorithm for Ward Clustering ?
Hi R people,
i'm looking for the Reciprocal Nearest Neighbour algorithm applied to
Ward clustering;
I know that it is explained in details in the following book:
Downs, G. M.; Willett, P. In Advanced Computer-Assisted Techniques in
Drug Discovery; van de Waterbeemd, H., Ed.; VCH: Weinheim, 1994; Vol. 3.
but cannot order copies it without knowing the pages involved; could
someone
2014 Jun 30
1
How to combine/join/merge etc PCA and Cluster?
Hello everybody,
I Would like to get some help to plot together, Principal Components
Analysis (PCA) and clusters.
I am handling environmental data from 25 locations spread across 5
different ecosystems.When grouped into 5 clusters, locations from different
ecosystems are arranged in the same group.
So, I want to plot together PCA and Clusters, in a such way that locations
belonging to the same
2002 Apr 29
2
cluster analyses
I'm clustering rather large data sets and would like to cut the dendrograms
to get a better view of specific components. I calculate the dissimilarity
matrix using daisy() because I have a mixture of variable types: factors,
ordered factors and numerical variables. If I want one dendrogram, I use
agnes() for the agglomerative nesting and pltree() to draw the dendrogram.
That way, I get the
2002 Jul 19
2
Plotting a section of a dendrogram
> I have performed clustering analysis with hclust (Ward's method) on a
> database of 800 samples. As you may imagine the full dendrogram is not
> really readable. I have obtained groups with cutree. I would like to
plot
> sub-sections of my big dendrogram to show group 1, group 2 and so on.
I don't think R has anything like subtree in Splus, unfortunately. I
think what has