similar to: Biclust package: drawHeatmap()

Dear all, I share the problem Linda Garcia and Ram Kumar Basnet described; I have a biclust object, containing several clusters. For drawing a heatmap, it is possible to specify the cluster to be plotted. However, I'd like to extract the clusters in this manner: Cond.1 Cond.2 Gene - value - value just like drawHeatmap specifies each cluster. Is there a way to extract single

Hi, I wanted to compare the quality of biclusters obtained from the various biclustering algorithms. Is there a function/metric in biclust (or some other package) that will enable me to do this? thanks! [[alternative HTML version deleted]]

I have a dataframe in which I have values 0-255, I wish to transpose them such that: if value > 127.5 value = 1 if value < 127.5 value = -1 I did something similar using the "binarize" function of the biclust package, this transforms my dataframe to 0 and 1 values, but I wish to use -1 and 1 and looking for a way in R to do this. Brian

I have a dataframe that has a header like so: class value1 value2 value3 class is a factor the actual values in the columns value1, value2 and value3 are 0-255, I wish to binarize these using biclust. I can do this like so: binarize(dataframe[,-1]) this will return a dataframe, but then I lose my first column class, so I thought I could combine it like so: dataframe <-

Hi all, I've got clusters and would like to match individual records to each cluster based on a sum of squares deviation. For each cluster and individual, I've got 50 variables to use (measured in the same way). Matrix 1 is individuals and is 25000x50. Matrix 2 is the cluster centroids and is 100x50. The same variables are found in each matrix in the same order. I'd like to

Hello, 1. After I generate a 100x50 matrix by x3<-matrix(0,100,50);for (i in 1:100) {x1<-rpois(50, mu[i]);x2<-x1; x2[runif(50)<.01]<-0; x3[i,]<-x2}, 2. I want to calculate means and sample variances of each row and create a new matrix 100x2; 3. I then want to repeat above procedure 500 times so that eventually I will have 500 100x2 matrices. Would someone mind helping me to

This is a fairly entry level question - so any guidance on this would be appreciated... I have two sets of residuals, one of 100 values (A), and one of 10,000 values (B). There are 50 paired sets of these values. The data is in the form of two matrices (100x50 and 10,000x50). The goal is to correlate the residuals from A and B, to identify a those B values that go up when a single A value goes

x11perf is a standard X11 tool for measuring how many times per second a given X11 request can be made. This release adds one new general option: -pause <s> pause for <s> seconds between each run and several new test options: -crgb10text Char in 80-char rgb core line (Charter 10) -crgb24text Char in 30-char rgb core line

Hi R users,   I am trying to do two-way clustering (using information of both observation and variables). Is there any package available in R. Another querry, if somebody can provide related information (website) regarding this statistics, it will be great. Thanks in advance.   Regards,   Ram Kumar Basnet, Wageningen University. [[alternative HTML version deleted]]

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 My ultimate goal is to best fit time series by comparing AICs and BICs (as in Bayesian) from arima() and nnet(). I looked at the arima.R source code, but I am afraid I do not understand it. What I only miss really is the number of parameters p, where: AIC = n*log(S/n) + 2*p with S the squared residuals and n the number of observations. Can I get p

Hi, I was trying to get hyperlinks using xtable, but couldn't get the hyperlinks to function properly. For example, if I use ## Try to link NY times website to every figure in column 4 mat <- matrix(1:43,6,5) mat[,5] <- "http://nytimes.com" for(i in 1:nrow(mat)){ strr <- paste('<a href="', mat[i,5],'">', mat[i,4], '</a>',

Dear R-help, I have used the regsubsets function from the leaps package to do subset selection of a logistic regression model with 6 independent variables and all possible ^2 interactions. As I want to get information about the statistics behind the selection output, I?ve intensively searched the mailing list to find answers to following questions: 1. What should I do to get the statistics

Hi All, I am new in R and trying to simulate random normal 2D field with mean trend say north-south. My domain is 10x10 grid and I am trying to use mvnorm but do not know how to specify the domain and the mean field. I would appreciate any help. Cheers, SK --------------------------------- [[alternative HTML version deleted]]

Hi, I was trying to make a graph using trellis, and my code is: ----------------------------------------------------------------- library(lattice) makeGraph <- function(){ trellis.device() tbg <- trellis.par.get("background") tbg$col <- "white" trellis.par.set("background",tbg) # Test Data mfr <- matrix(sample(1:100,50,replace=T),ncol=2)

Dear r-help, I have a matrix, suppose, 10x10, and I need the matrix 5x5, having in each cell a mean value of the cells from the initial matrix. Please, point me to a function in R, which can help me doing that. Digging the documentation and mail archives didn't give me a result. Thank you. --- Best regards, Vladimir mailto:wl at eimb.ru

On Thu, Dec 6, 2012 at 11:59 AM, Greg Fitzgerald <garious at gmail.com> wrote: > Maybe I'm jumping the gun, but some initial thoughts after browsing the MC > layer changes: > Greg, it's great to have early comments on this. > * .bundle_align_start -> .bundle_align_mode N ? > * .bundle_align_end -> .bundle_align_mode 0 ? The initial proposal does not cover

Hi, I was trying to get a graph in lattice with the following data frame (7 rows, 5 cols): chr start1 end1 meth positive 1 1 10 20 1.5 y 2 2 12 18 -0.7 n 3 3 22 34 2.0 y 4 1 35 70 3.0 y 5 1 120 140 -1.3 n 6 1 180 190 0.2 y 7 2 220 300 0.4 y I wanted the panels to be organized by 'chr' -

Dear all, I'm a bit confused about the output from functions that generates random values, e.g. rpois. I'm using 0.65.1 on Digital UNIX alphaev6. If I say > rpois(10,5) output is not unexpectedly: [1] 4 6 5 7 6 5 2 2 5 3 but I figured that if I go: > rpois(10,1:10) I would get a 10x10 matrix as output, with random values for each of the vector elements in the row vectors, but

Hi Could somebody please explain the following to me: If x is a 10x10 matrix, typing x[3] prints all 10 values of column 3, although the length of the vector =1. Why? x[,3] and x[[3]] both give all 10 values of column 3, length=10. What is the difference between these two, actually? Thanks Karen Kotschy Centre for Water in the Environment Department of Botany University of the Witwatersrand

Hi there, I'm currently trying to install a server with Centos 4.3 x86_64. I have issues installing drivers from a Driver disk, I got a driver(2810SA) from the Adaptec site, I started it up with "linux dd" It reads the disk fine .... I can see the aacraid module in the list but as soon as I choose it. Then I get a screen saying "Do you wish to load more Driver Disks?" I