similar to: dimnames(x) <- dn error

i have a matrix with the following dimensions 136 3 and it looks something like [,1] [,2] [,3] [1,] 402 675 1.802758 [2,] 402 696 1.938902 [3,] 402 699 1.994253 [4,] 402 945 1.898619 [5,] 424 470 1.812857 [6,] 424 905 1.816345 [7,] 470 905 1.871252 [8,] 504 780 1.958191 [9,] 504 848 1.997111...............

Hi, I'm trying to calculate euclidean distance for my matrix rx1. Its a big matrix with 947 elements. However when i do the following, for(k in 1:947) for(m in (k+1):947){ A =rbind(A,c(k,m,ED(rx1[,k], rx1[,m]))) } I get the following error: ED(rx1[,k], rx1[,m]) : subscript out of bounds I checked for k in 1:100 and it runs fine; its a huge matrix and takes atleast an hour to run before I

Hi, I am very new to R. Just started yesterday. I have to generate a sequence of 40 random treatments using permuted block randomization with a block size of 8. Then I have to plot moving averages for the resulting sequence. I have tried the sample function but I dont know if wht i did is right or not > sample(c(1,1,1,1,2,2,2,2),8) Any ideas please? -- Ayesha Khan MS Bioinformatics Dept. of

Hi All I am tying to create a user in SAMBA 4 AD with ldapadd, but its not allow me to add multiple mail attributes, here is my ldif of user. dn: CN=ayesha,CN=Users,DC=samba4pdc,DC=net objectClass: top objectClass: person objectClass: organizationalPerson objectClass: user cn: ayesha name: ayesha sAMAccountName: ayesha userPrincipalName: Ayesha Umar objectCategory:

Ho Mourik Thanks for your reply, any other attribute which we can duplicate? Br. Umar On Fri, Jan 23, 2015 at 1:47 PM, mourik jan heupink - merit < heupink at merit.unu.edu> wrote: > Hi, > > In AD, the attribute mail can only exist once. > > MJ > > On 01/23/2015 05:27 AM, Umar Draz wrote: > >> Hi All >> >> I am tying to create a user in SAMBA 4

Hi, I have tried looking at the archives but havent found any answer that works till now (Sorry if i have missed anything) I am a newbie to R and i am trying to carry out hierarchical clustering using hclust -> as.dendrogram and then plotting the results as a dendrogram using the plot function plot(object). My question is : In the function "plot", can one decrease the leaf label

Hello everyone! I have two questions regarding cluster analysis with the package 'cluster' : 1. I have a dissimilarity matrix in csv format, and I would like to use it to generate a dendogram using 'hclust'. How do I make that matrix compatible with the function? I think it has to be similar to the objects generated by the 'dist' function. Any ideas? 2. Does

Hi. I am getting an "unexpected symbol" error, which I haven't gotten before. I have checked my data and searched the FAQ. I hoping someone has a suggestion on what I might be doing wrong? Thanks! A. Gray Fisheries Consultant Here's the code I'm using and the error: > 0708smolts <- read.csv("C:\Documents and Settings\ayesha\My

On 23/01/15 09:44, Umar Draz wrote: > Ho Mourik > > Thanks for your reply, any other attribute which we can duplicate? > > Br. > > Umar > > On Fri, Jan 23, 2015 at 1:47 PM, mourik jan heupink - merit < > heupink at merit.unu.edu> wrote: > >> Hi, >> >> In AD, the attribute mail can only exist once. >> >> MJ >> >> On

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.

Hi,   I need to generate a heatmap on a square matrix and wouldn't want to reorder the columns and the rows on the heatmap display.    I have used the options Rowv=NULL and Colv=NULL but doesn't seem to work. Following is a snippet of the heatmap function i am using. args <- commandArgs(); inputfile <- args[2] imgfile   <- args[3] bitmap(imgfile, height=15, width=15, res=100,

I am using R for hierarchical clustering of a number of documents. I have a distance matrix on which I have applied hclust method. When I plot the result of hclust method, I can see the dendogram plotted. What I need now is the dendogram stored as a tree in a data structure. My goal is to automatically label all internal nodes. For that, I need to know, which leaf nodes make a first level

Hello. I have the following distance matrix between 8 points: [1,] 0.000000 3.162278 7.280110 8.544004 7.071068 9.899495 6.403124 8.062258 [2,] 3.162278 0.000000 5.000000 6.403124 4.472136 8.944272 6.082763 8.062258 [3,] 7.280110 5.000000 0.000000 1.414214 1.000000 5.000000 4.242641 5.830952 [4,] 8.544004 6.403124 1.414214 0.000000 2.236068 4.123106 4.472136 5.656854 [5,] 7.071068 4.472136

Hi everyone, I am using the fastgreedy.community function to get the $merges matrix and the $modularity vector. This serves my purpose of testing modularity of my graph. But I am "greedy" to plot the heat map and dendrrogram based on the $merges dendogram matrix. I know that heatplot does the graphics part but I am not sure if the dendogram generated by the heatplot will match the one

The data "one" is a vector of 553 observations agglone<-agnes(one, metric = "manhattan", stand = TRUE) plot(agglone,which.plots=2, nmax=150) My problem is in the dendogram, I can not see the nodes because it is too crowded. I have attached the diagram. Any help is more than welcome. Thank you a lot!!!

Dear all, I need to make dendogram from read count in a csv file across 34 samples including biological replicate. Please share R code or package to do this. Do I also need to normalized read count before using read data? Thanks [[alternative HTML version deleted]]

Dear R I recently performed a cluster analysis. It produced the dendogram no problem but unfortunately the font size of the row.names were all cluttered due to their large size So I tried to change the font size using plclust(cluster.results, labels=iris$specie, cex=0.8) and R came back to me saying Error in plclust(cluster.results, labels = iris$specie, cex = 0.8) : unused argument(s)

I have used heatmap to visualize my microarray data. I have a matrix of M-values. I do the following. #The distance between the columns. sampdist <- dist(t(matrix[,]), method="euclidean") sclus <- hclust(sampdist, method="average") #The distance between the rows. genedist <- dist(matrix[,], method="euclidean") gclus <- hclust(genedist,

I want to do hierarchical cluster analysis to compare 10 groups of vectors with five vectors in each group (i.e. I want to make a dendogram showing the clustering of the different groups). I've looked into using dist and hclust, but cannot see how to compare the different groups instead of the individual vectors. I am thankful for any help. Anders

Dear All, I am trying to find a way to plot a dendogram in reverse, that is, if the terminal leaves are labelled 1-10 bottom to top (or left to right), I would like to be able to plot it in a way such that if would display 10-1 bottom to top or left to right. Any idea how to achieve this? Thanks in advance, r. Dr. Rafael Najmanovich European Bioinformatics Institute Wellcome Trust