similar to: Getting error in dendogram based on gene expression

I am trying to make dendogram based on gene expression matrix , but getting some error: I countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F) colnames(countMatrix) count_matrix <- countMatrix[,-1] # remove first column (gene names) rownames(count_matrix) <- countMatrix[,1] #added first column gene names as rownames) >

There are two line 216 and 218 Three development stages 5 WEEK (5W), 7W, 9W. Three tissue: Ca, Co, Pa each with 2 biological replicate. With two biological replicate. I want to do differential gene expression analysis using DESeq2 so I tried these codes after reading about DESeq2: ,my aim is to do the pairwise comparison. how to make colData and design formula. library("DESeq2")

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]]

Hi , I am trying to open vignette DESeq2 but getting below error: > vignette("DESeq2") > START /usr/bin/evince "/usr/lib64/R/library/DESeq2/doc/DESeq2.pdf" Cannot parse arguments: Cannot open display: xdg-open: no method available for opening '/usr/lib64/R/library/DESeq2/doc/DESeq2.pdf' -- *Yogesh Gupta* *Postdoctoral Researcher* *Department of Biological

Hi... I have a dataframe with n columns and n rows. I need to find how many rows contains zero raw read count across all column. Thanks -- *Yogesh Gupta* *Postdoctoral Researcher* *Department of Biological Science* *Seoul National University* *Seoul, South Korea* [[alternative HTML version deleted]]

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

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!!!

Hello does anyone know what algorithm is used to produce the hierarchical clustering in the gplots package using the function heatmap.2? I think it may be the complete linkage clustering algorithm, but I can't find a source that seems reliable. Thank you and sorry if I posted this in the wrong place. If I have, please let me know and I will move it to the appropriate list. -- View this

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

Dear R-help, I have performed a hierarchical clustering on some data that I have and would like to know some nice ways of visualizing it. I have 2 related questions: i) How to color the labels AND the terminal branch of a dendogram? This is my inelegant way of just getting the colored labels. data(iris) # Formatting data into required format ir <- iris[ ,-5] ir.class <- c(

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)

Hi, I have trouble with the heatmap function (package stats). The row labels are wrongly ordered and don't correspond to the Rowv dendrogram. I know there is a bug with the heatmap fonction. Emmanuel Paradis (http://tolstoy.newcastle.edu.au/R/e2/help/07/05/16227.html )suggested a modification to fix it but in my case the row labels are still wrongly ordered. Heatmaps with 2 phylograms have

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate

Howdy, R Grues I have enjoyed R, but I cannot solve one problem easily. Please help my problem. When I tried the R script, I got the following Error. This error results from input data file exported through a Excel spreadsheet software. Error in step(lm(pop.rate ~ as.numeric(year) + as.factor(policy) + as.numeric(nation.grant) + ?: ??number of rows in use has changed: remove missing values?

Dear All, I am learning R so it's a very simple problem but I do not understand while I am not able to generate a graph from two vectors. when I type this code, it generates a very nice graph. pdf("mygraph.pdf") > attach(mtcars) > plot(wt,mpg) > abline(lm(mpg~wt)) > title("Regreesion of mpg") > detach(mtcars) > dev.off() But I am trying to create a

I did a make update. I thought I was running the newest version of compiler-rt. But now I can't even get the project to build. I get the following error: i386-redhat-linux-gnu-clang++: clang/llvm/include/llvm/ADT/SmallVector.h:544: typename llvm::SmallVectorTemplateBase<T, llvm::isPodLike::value>::iterator llvm::SmallVectorImpl<T>::insert(typename

+kcc, llvmdev I think your compiler-rt checkout is out of date, because r188635 is supposed to fix that exact issue. On Mon, Aug 19, 2013 at 9:16 PM, Sharma, Yogesh < Yogesh.Sharma at saabsensis.com> wrote: > Sorry about that. I forgot a d:**** > > ** ** > > ldd (GNU libc) 2.12**** > > Copyright (C) 2010 Free Software Foundation, Inc.**** > > This is free

Hi all , I'm running Debian Etch . I just finished configuring SAMBA as PDC to authenticate against LDAP server which works. The system in question uses default debian etch packages. As My Linix/unix accounts can authenticate against it. The LDAP works. I Used the default shipped smbldap-populate script to setup SAMBA. Everything seems to work as Anonymous User or as user

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

Hello R Users, Whether 'R' can import Netcdf format data files ?? Any package in 'R' that can help me on this front ?? Many thanks in advance, Regards, Yogesh -- =========================================== Yogesh K. Tiwari, Max-Planck Institute for Biogeochemistry, Postfach 10 01 64, D-07701 Jena, Germany Office : +49 3641 576376 Fax : +49 3641 577300 Home : +49