Displaying 20 results from an estimated 500 matches similar to: "pvclust:a general and a specific question"
2007 Jun 08
2
How to do clustering
Dear List,
I have another question to bother you about how to do clustering.
My data consists of 49 columns (49 variables) and 238804 rows.
I would like to do hierarchical clustering (unsupervised clustering
and PCA). So far I tried pvclust (www.is.titech.ac.jp/~shimo/prog/*pvclust*
/)
but I always had the problem like for R like "cannot allocate the memory".
I am curious about what
2010 Jul 20
1
p-values pvclust maximum distance measure
Hi,
I am new to clustering and was wondering why pvclust using "maximum"
as distance measure nearly always results in p-values above 95%.
I wrote an example programme which demonstrates this effect. I
uploaded a PDF showing the results
Here is the code which produces the PDF file:
-------------------------------------------------------------------------------------
s <-
2006 Jul 06
0
pvclust Error:NA/NaN/Inf in foreign function call (arg 11)
Hi all,
I'm new to R and I'm struggling to decipher an error message. Briefly, I am trying to use the pvclust package to do hierarchical clustering of some CGH data. The data is from the Progenetix CGH database. It is arranged as a table where each column is a single case and each row is a single chromosome band. The value in each cell is either 0, 1, 2, or -1. Corresponding to no change,
2014 Jul 28
1
Split PVClust plot
Dear All
I'm using PVClust to perform hierarchical clustering, for the output plot I can control most of the graphical I need, however the plot is large and I would like to split it vertically into two panels one above the other. Is there a way to plot only part of a PVClust plot, I tried to convert it to a dendrogram with
result2 = as.dendrogram(result)
however I get the error message
2009 Jul 09
0
Node colors in pvclust
Is there a way to assign color to nodes as with
hclust/as.dendrogram/dendrapply when using pvclust?
The problem is that as.dendrogram isn't working on the pvclust objects.
library(pvclust)
pvc <- pvclust(matrix, nboot=1000)
plot(pvc)
--
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2010 Aug 09
0
Fwd: RE: pvclust function
You should reply to the list, not just me, and even more because I
cannot really help you!!
My guess (but I don't know this package, and even less this function) is
that pvclust() is expecting a matrix as the first argument. However,
"cluster" is no data, it is a function. Why, I don't know. Take a closer
look at ?pvclust, especially the "usage",
2011 Mar 05
1
pvclust crashing R on Ubuntu 10.10
Hi all
I am writing to you with a question regarding the pvclust package. And
yes, before the usual people produce their usual
contact-the-package-maintainers line, ye, I tried that but the emails
one can find on the web either bounce or are not responded to. Also,
yes, this error has already been reported as a bug but been shot down
as not reproducible
2010 Aug 10
2
p-values with pvclust
Hi,
if you look at the first image (Image1) you see that there are 2 main
clusters 7 and 8
I wanted to use pvclust to calculate a p-value whether these clusters are
due to chance
or statistically significant. Unfortunately pvclust does not provide a
p-value for the first
brunch (7 and 8).
So I added a row to my matrix which is very different to the rest of the
data to create an additional
2008 Jun 16
0
pvclust distance matrix
Hello,
I am attempting to assign significance levels to a UPGMA cluster analysis as part my doctoral research. The pvclust function works well but doesn't include the similarity index I need (morisita's) as an option for computing a distance matrix. Morisita's is available in vegdist in the VEGAN library but I am having a hard time getting the vegdist function to "direct
2006 Jul 10
2
pvclust missing values problem
Hello all,
I posted a question to this list last week and received no response. I am unsure if this means no-one knows the answer or if I posed the question badly. I'm going to assume I posed the question badly and try again. I am new to R so it is quite likely it's a very naive question, however if there is something blindingly obvious that I am missing or if there is another resource I
2007 Dec 07
1
pvclust warning message
Hi all
I am trying to perform the follwing:
fit<-pvclust(wq, method.hclust="ward", method.dist="euclidean")
but get a strange error message that I just cant figure out.
Has anyone come across this? Any help would be most appricieated
Error in hclust(distance, method = method.hclust) :
NA/NaN/Inf in foreign function call (arg 11)
In addition: Warning message:
NAs
2008 Jul 23
0
pvclust
Hello there,
Here's a question regarding p-values on clusters produced by hierarchical
cluster analysis. A web search led me to the program pvclust to tackle this
problem. But when I run the problem I get strange results. The 'AU'
(approximately unbiased) p-values are very different from the 'BP' values
(ordinary boot-strap) p-values. The AUs commonly are in the 80-100
2008 Nov 22
1
Nested Clade Analysis
Hi
Wondering if anyone knows of a package that does Nested Clade Analysis?
Thanks
--
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2010 Jul 19
1
possible bug in ape::extract.clade()
Hi,
I was recently splitting some massive phylo class objects with extract.clade()
and noticed what appears to be a bug in how tip labels are copied from the
full tree to the pruned tree. This possible bug was also mentioned here:
http://www.mail-archive.com/r-sig-phylo at r-project.org/msg00537.html
An example:
library(ape)
set.seed(5)
x <- matrix(rnorm(100), ncol=10)
p <-
2012 Dec 05
1
request
Dear Dr. bernhard
cc. r-help
Thank you very much for deverlopping rneos package. I read the document of
rneos.
however, due to my inability, i could not figure-out how to connect with
neos server from R environment.
let me explain the steps, i took. my laptop is using wireless of my
laboratory. to connect the internet, i need proxy address and specific port
(that i have mentioned in protocols in
2007 Jul 09
1
The Camellia block cipher for OpenSSH 4.6p1.
Hi,
I implemented a patch for porting the Camellia block cipher to
one of the OpenSSH-usable cipher. Camellia is one of the approved
encryption methods of NESSIE and has specified in several RFCs.
I put the patch at:
http://www.is.titech.ac.jp/~yanagis0/text/camellia/openssh-4.6p1-0.2.patch
in http://www.is.titech.ac.jp/~yanagis0/text/camellia-e.html.
I hope you will enjoy this patch and
2010 Sep 21
1
partial dbRDA or CCA with two distance objects in Vegan.
I am trying to use the cca/rda/capscale functions in vegan to analyse
genetic distance data ( provided as a dist object calculated using
dist.genpop in package adegenet) with geographic distance partialled out
( provided as a distance object using dist function in veganthis method
is attempting to follow the method used by Geffen et al 2004 as
suggested by Legendre and . FORTIN (2010).
I
2011 Nov 15
0
Bootstrap values for hierarchical tree based on distaance matrix
I would like to get an hierarchical clustering tree with bootstrap values
indicated on the nodes, as in pvclust. The problem is that I have only
distance matrix instead of the raw data, required for pvclust. Is there a
way to get it?
fit1 <- hclust(dist) # an object of class '"dist"
plot(fit1) # dendogram without p values
library(pvclust)
fit2 <- pvclust(raw.data,
2012 Dec 06
1
clustering of binary data
Good morning,
I am analyzing a dataset composed by 364 subjects and 13 binary variables
(0,1 = absence,presence).
I am testing possible association (co-presence) of my variables. To do
this, I was trying with cluster analysis.
My main interest is to check for the significance of the obtained clusters.
First, I tried with the pvclust() function, by using method.hclust="ward"
and
2010 Aug 09
1
(no subject)
Hi there,
I have been trying to use the "pvclust" package but have been having
some difficulties. This is the first time I have used R so I am sure the
mistake I am making is a basic one. The data I have is a distance matrix
and I have been using the command; fit <- pvclust(cluster, nboot=1000,
method.dist="euclidean") to try and perform hierarchical clustering with