search for: gisar

Dear all, I am trying to create a web interface using Perl-CGI to call R plots and to display them. The following codes works perfectly fine when I copy and paste into the console directly or if I save it into script.file and then R --no-save < script.file producing the graphs. jpeg("graph.jpeg", width=400, height=400) plot(rnorm(100)) dev.off() Now, I put the line system("R

Dear R-help list members i would like to use R to produce clustering or partitioning of a dataset. I am trying to use the functions: - hierclust() of the package multiv -pam(), agnes() and fanny() of the package cluster But I cannot get any result because of lack of memory. Would you know any clustering function not to greedy in memory? I have tried to expand my memory limit with memory.limit()

...1438 Aladdin Ghostscript 6.0: Unrecoverable error, exit code 1 #################### Can anyone help please ? R Version 1.6.1 (2002-11-01) Aladdin Ghostscript 6.0 R_GSCMD : /usr/local/bin/gs Platform: SunOS Release : 5.8 Version : Generic_112953-02 Machine : sun4u -- Adaikalavan Ramasamy gisar at nus.edu.sg Research Assistant http://giscompute.gis.nus.edu.sg/~adai Microarray & Expression Genomics Tel: 65-6827 5247 Information & Mathematical Sciences Fax: 65 6827 5204 Genome Institute of Singapore www.genomeinstitute.org

Dear all, I've taken a subset of data from a data frame using crb<-subset(all.raw, creek %in% c("CR") & year %in% c(2000,2001) & substrate %in% ("b")) this works fine, except that all of the original factor levels are maintained. This results in NA's for these empty levels when I try to do summaries based on factors using by(). Is there a simple way to drop

How can I best achieve the following (works in Splus): filenames <- dos("dir *.sasb7dat /b") What I am asking, more generically, is: how can I capture the output of a DOS command in R? I have tried using system("COMMAND.COM /c dir /b", intern=T, show.output.on.console=T) where intern: a logical, indicates whether to make the output of the command an R

Just out of curiosity, can some please explain the following return NA. x <- 6 var(x) y <- c( NA, NA, 10000 ) var(y, na.rm=T) Unless I am seriously misguided, I believe that the variance of a single number (i.e. a constant) should be zero. Thanks. Regards, Adai.

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(

I am attempting to replicate what Cluster 3.0 and Treeview (both by Mike Eisen) to cluster both microarray genes and arrays does using R with hclust. I basically utilized the plot.mat function in sma library with some layout() and hclust(). 1. Can I know if some has already written such a function or available in some package. 2. If not, would appreciate if someone could take the time to test

Dear all, I am trying to compile the package e1071 (version 1.3-11) with R CMD INSTALL. I tried with R 1.7.0 on Redhat Linux 2.4.7-10 and R 1.6.2 on Linux 2.4.9-34smp but keep getting the same error message during configure : WARNING: g++ 2.96 cannot reliably be used with this package. Please use a different compiler. Can anyone help me with this or at least point me in the right direction ?

Dear all, I fit independent GLMs for a 2x2 factorial problem on the data matrix of size 9500 x 12 (genes x arrays) and get 9500 observed t-values using the apply() function. Now, I wish to get the permutated p-values. Therefore I random sample the class labels and perform the glm fitting to get the t-values from which I can get the p-values. This is done using a for() loop. Is there a more