similar to: calling R from Perl

I am running R 2.0.0, GOstats 1.1.1 and GO 1.7.0, and when I use the function GOHyperG, I have the following error: w1<-as.list(hgu95av2LOCUSID) w2<-unique(unlist(w1)) set.seed(123) myLL<-sample(w2,100) xx <- GOHyperG(myLL) Error in mget(x, env = GOTERM, ifnotfound = NA) : recursive default argument reference In fact first I tried this function with my locusId ' list (with

I have released the new module Statistics::R and need some feedback of it's status. This will permit the control of the the R (R-project) interpreter through Perl in different architectures and OS. You can for example, start only one instance of the R interpreter and have different Perl process accessing it. What will save the initiation time of R and memory. Soo, I will appreciate if some

Hello, I basically want to use R-help, and post some problems which I am facing. The Ref is a well known Genome Biology paper "Bioconductor: open software development for computational biology and bioinformatics" by Robert C Gentleman et al., 2004. Generating Heatmaps till Fig2 is working so I think esetSel is not the problem.. However, for generating the Figure 3, for GO annotations the

hi, all: Just wonder if there is any suggestions in how to get around this cbind error. I created two character lists with identical length. First tried combine the lists together with cbind, then convert the lists to matrix, and tried again. Both faied. Any fix to merge the two lists/matrices? ll<- multiget(ftID, hgu95av2LOCUSID) > class(ll) [1] "list" > sym <-

Hi!I'm doing a little data importing from .cel files, > setwd("/home/mandova/celfiles") > mydata<-ReadAffy() Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) : unused argument(s) (extended = TRUE) Then I tried > filenames<-paste("GSM",c(seq(138597,138617,1)),".cel",sep="") >

I am getting the following error in my script. I am very very new to R and have obtained this script from another person. #read file in (dummy data) starburst.plot<-function(affy.fold, affy.FDR)(ifelse( ((affy.fold) >=0), -1*log10(affy.FDR), 1*log10(affy.FDR))) starburst.plot<-function(meth.fold, meth.FDR)(ifelse( ((meth.fold) >=0), -1*log10(meth.FDR), 1*log10(affy.FDR))) At my next

Anybody used the above phone with asterisk I have one working ok for calls, but having a problem with voice mail. Using either the 'Voice mail function key' or dialing 88 (for my system) just gets me to Call Terminated Asterisk CLI shows the error message 'unable to get User name' My Grandstream works ok, asking for User name, then Password Any ideas ? -- Clive Email :

Hi, I am looking for a way to find out the version information of installed R packages. ex: >library(affy) >SOME_COMMAND_FOR_VERSION(affy) I know I can do either getRversion() or R.Version() could give me the version of R. I assume there must be a way for me to get version information for the add-on paclages,right? Thanks! Yupu

Hi, I decided to upgrade to 1.8 today... :-) Anyway, we are writing our own package that is dependent on a bioconductor library - 'affy'. I've checked and when I fire up R, library(affy) behaves as expected... so it all seems to be installed and OK... In the DESCRIPTION file in my package source I have the line: Depends: affy When I run R CMD check simpleaffy I get to: ... *

Hi, all. Something strange happened to my ESS. I use Mac OS X. When R is used in stand alone mode, it recognizes external libraries like "affy", "e1071" etc. However, when R is invoked through ESS in Emacs, it produces errors like: Error in library(affy) : There is no package called 'affy' Interestingly, I remember I successfully used these libraries through ESS in

Hello, I am trying to install affy package in R as follow: >R CMD INSTALL -l lib ~/rstuffs/affy_1.4.32.tar.gz Then I get an error at the end: Warning message: There is no package called 'Biobase' in: library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, [1] "ProgressBarText" [1]

Hi all I am wondering if anyone has had a similar trouble to this: The timeout arguments in the dial command does not work. The caller does not get disconnected when the timeout reaches zero. I am not sure if this is a chan_capi issue, or a asterisk issue. I am using CVS-head and chan_capi CVS head also. Any suggestions or help will be appreciated. Thanks Clive

Hi, I have been using the prcomp function to perform PCA on my example microarray data, (stored in metric text files) which looks like this: 1a 1b 1c 1d 1e 1f ...................................................4r 4s 4t g1 1.2705 1.2766 ...........................................................2.0298 g2 0.1631

Hi, I download Statistics::R from http://search.cpan.org/~gmpassos/Statistics-R-0.02/ I am going to combine R with perl. but it keeps give the error msg: ERROR: unknown GUI none & stop running script. I feel very strange, because previously it works. my perl version is 5.8.6 my R version is Version 2.2.1 Is there anybody know about it? Thanks a lot. Nina [[alternative HTML version

I think this is the fourth attempt to send this blessed message, so let's hope this gets through without any 'unprocessed' or 'ignored' in-lines on auto-reply. I wish to report to you some strange problems I'm experiencing with installing packages directly into my -R- 2.15.1 (there is an indirect solution, which I note below). First, here's some essential information:

Hello all, I am trying to make a genome association plot for p-values related to SNPs and was fortunate to find that R contains a package that produces Manhattan plots which is what's preferred for my current project. The function mhtplot() is found in the 'gap' package which I installed in R 2.11.1 on Windows. I thought I'd test out the function first with the examples they

Hi I was doing some bandwidth testing, and my incomming usage is 36% more than my outgoing bandwidth. The setup is IAX2 trunking using GSM codec. Is there any obvious reason I am overlooking to figure out why there is such a big difference between the two.? I am using CVS-head September 3rd, maybe there is a version skew? Any suggestions will be appreciated. Thanks Clive

I have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and

I have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and

Hi Having my first go at compiling Asterisk from cvs source. Compiled and installed zaptel ok Running make asterisk returns the following error message /usr/bin/ld cannot find -lssl collect2: ld returned 1 exit status The last part of the compile messages on screen are- editline/libedit.a db1.ast/libdb1.a stdtime/libtime.a -ldl -lncurses -lm -lresolv -lssl There is obviously something I have