similar to: pvclust

Hello: As someone making the move from STATA to R, I'm finding it difficult at times to perform basic tasks in R, so forgive me if I've missed an obvious and easily obtained solution to my problem. I've searched the help guides and the archives and have not been able to find a solution that works. I have a data frame with thousands of observations that looks something like this:

I realize questions about packages should go to the package maintainer, but perhaps I have an old email address (suzuki3 at is.titech.ac.jp) Also I have both a general, and a specific, question. 1) General question: i've used pvclust before to assess significance of clusters and got reasonable results. However, on a new data set (see below) the results seem odd. I wonder if pvclust is a

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 <-

Dear All, Please provide me access to create wiki pages for my howtos Regards, Chinthaka -- Chinthaka Deshapriya (RHCE) Director/CTO Centre of Open Source Excellence Fossmart Private Limited. 163/1, Dutugemunu Street, Kohuwala, Colombo Sri Lanka http://www.fossmart.net Tel: +94-114-962-600 Fax: +94-112-823-429 Mob: +94-716-903-433 -------------- next part -------------- An HTML attachment

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,

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 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

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

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

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 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 All, We successfully installed MFC/R2, chan_unicall.so with asterisk ver 1.2.6. asterisk is loading properly and we can see US show channels working fine. We are using digium Te120P card. Now we are trying to setup E1 link with Nortel DMS 100, which is resides at one of telco provider in Sri Lanka. But we don't know what is the exact protocol varient to use. Is anyone help us out on this

Hi, I am a Computer Science and Engineering student at University of Moratuwa, Sri Lanka. I went through the project proposals of Xapian at Gsoc 2014. I found the project "c# binding improvement", very attractive for me to start up with committing to open-source community. And then found that is is not taken by any student. Please, some one can help me to start on this. I have 3 years

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,

In correspondence with the other ram_calc implementations. Signed-off-by: Roy Spliet <nouveau at spliet.org> --- drivers/gpu/drm/nouveau/nvkm/subdev/fb/ramgf100.c | 37 ++++++++++++----------- 1 file changed, 19 insertions(+), 18 deletions(-) diff --git a/drivers/gpu/drm/nouveau/nvkm/subdev/fb/ramgf100.c b/drivers/gpu/drm/nouveau/nvkm/subdev/fb/ramgf100.c index 093223d..fffd01a 100644 ---

Hi Louis, I don't have a FW enabled on my PC. I even tried to disable the FW on my all my DC's I can telnet to port 389/636/53, they are all open and goes through to my all DC's. Primary DC # Global parameters [global] workgroup = DOMAIN realm = DOMAIN.CORP netbios name = ##SELECTION_END##ZACPRDC002 server role = active directory domain controller idmap_ldb:use rfc2307 = yes

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

Hai Eben (victor), ? Great to hear that, you opened TCP 53 ? edns?tcp/53?packet size 4096. dns??? udp/53 packet size 512? ? having that right helps?a lot, but only that is often not enough.? This is why i add the options also to resolv.conf and?bind.? ? test a bit, and see what works best for you. ? Great weekend. ? Greetz, ? Louis Van: Eben Victor [mailto:eben.victor at gmail.com]