similar to: pvclust crashing R on Ubuntu 10.10

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 <-

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

Hi, I have a microarray dataset of dimension 25000x30 and try to clustering using hclust(). But the clustering on the rows failed due to the size: > y<-hclust(dist(data),method='average') Error: cannot allocate vector of size 1.9 Gb I tried to increase the memory using memory.limit(size=3000), still got the same error. I also tried agnes() from cluster package and pvclust() from

>From my book on corpus linguistics with R: # (10) Imagine you have two vectors a and b such that a<-c("d", "d", "j", "f", "e", "g", "f", "f", "i", "g") b<-c("a", "g", "d", "f", "g", "a", "f", "a",

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,

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

Full_Name: Stefan Th. Gries Version: R version 2.6.1 (2007-11-26) OS: Windows XP Home SP2 Submission from: (NULL) (68.6.47.105) Hi A simple computation results in integer overflow: These are the relevant vectors: > sum(cur.obs) [1] 110231 > colfreq other past perfect present progressive 14845 1222 4776 101347 2863 >

I have problem with integer overflow that I cannot understand. I have a character vector curr.lemmas with the following properties: length(curr.lemmas) # 61224 length(unique(curr.lemmas)) # 2652 That vector is the input to the following function: yules.k1 <- function(input) { m1 <- length(input); temp <- table(table(input)) m2 <- sum("*"(temp,

Dear all I use R for Windows 2.3.1 on a fully updated Windows XP Home SP2 machine and I have two related regular expression problems. platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor

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

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) -- View this message in context: http://www.nabble.com/Node-colors-in-pvclust-tp24405329p24405329.html Sent from the R help mailing list archive at

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",

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

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

Hi all I have problems installing rJava on my system. ######## My system: > R.version # at R prompt platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 8.1 year 2008 month 12 day 22 svn rev 47281 language R version.string R version 2.8.1

a) Numeric values may be either integers (signed 32 bit) or double precision (53 bit mantissa). b) Double precision constants are numeric with no decoration (e.g. 61224). Integer constants have an L (e.g. 61224L). c) 61224*61224 > 2^31-1 so that answer cannot fit into an integer. d) Exponentiation is a floating point operation so the result of 61224L^2L is a floating point answer that CAN

Hi, I wish to develop a web crawler in R. I have been using the functionalities available under the RCurl package. I am able to extract the html content of the site but i don't know how to go about analyzing the html formatted document. I wish to know the frequency of a word in the document. I am only acquainted with analyzing data sets. So how should i go about analyzing data that is not

Hi all I am running R 2.14.0 on Linux Mint 11 and want to use TeachingDemos but cannot update tkrplot. This is what happens: ############### In order to run * installing *source* package ?tkrplot? ... configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/share/R/include -I/usr/include/tcl8.5 -I/usr/include/tcl8.5 -fpic -O3 -pipe -g -c

dear all, I have some very long strings and would like to break up each long string into multiple strings with a fixed length, e.g. to break up abcdefghijkl into abc, def, ghi, jkl I tried a couple of commands but was not successful. Any help will be appreciated. Best, Jimmy -- View this message in context:

Hi all I have run into a case where I don't understand why predict.lrm and predict.glm don't yield the same results. My data look like this: set.seed(1) library(Design); ilogit <- function(x) { 1/(1+exp(-x)) } ORDER <- factor(sample(c("mc-sc", "sc-mc"), 403, TRUE)) CONJ <- factor(sample(c("als", "bevor", "nachdem",