similar to: GetBioC install issue

Hi, I have a data matrix of gene expression data from two groups that I would like to compare using the t-test. The data has been processed using RMA and transformed using log2. I would like to compare the two groups for each gene (N=10,000 genes) and have a result that lists the p-value for each test. Can anyone help me with the t.test setup for this analysis? Thanks, Rich Rich Roth, PhD

Hello, I am trying to install R/Bioconductor on a G4 Mac running OS X. I have successfully installed R so that a command window opens, but installation of the downloaded Bioconductor package is giving me trouble. After copying/pasting the Bioconductor installation script in to the window and typing getBioC(), I get the following error message. "Error in getBioC(): R not currently

I am receiving the following errors when trying to install gcrma and a number of other Bioconductor packages when the installWithVers flag is set to be TRUE. >source("http://www.bioconductor.org/getBioC.R"); >getBioC("gcrma", installWithVers=T); Running biocinstall version 2.0.7 with R version 2.5.0 Your version of R requires version 2.0 of Bioconductor. Loading

dear all, I try to update my Rversion fro 1.7.1 to 1.8.1 on linux. I have a problem when I try to install pacakges from Bioconductors with : source("http://www.bioconductor.org/getBioC.R") and getBioC(relLevel="release") somme errors append and when I make a library(affy) for example I obtain : > library(affy) Error in setIs("character",

Full_Name: H Deshmukh Version: 2.0 OS: 2000 Submission from: (NULL) (129.174.206.239) Can somebody tell me what is it that i am doing wrong,i was not sure whether to post BioConductor error here or not. Thanks >source("http://www.bioconductor.org/getBioC.R") > getBioC(libName = "all") Running getBioC version 1.2.65.... If you encounter problems, first make sure that

Hello useRs, I'm trying to install bioconductor on ubuntu edgy eft and R 2.4.0. I have some error messages during installation, in particular for the package "affy" : "Error: package 'affy' required by 'makecdfenv' could not be found" I have tryed to install 'makecdfenv' with the command : getBioC("makecdfenv") But I have this message

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]

Why am I seeing the following in R-devel (sept 2, 2006 build) on opensuse 10.1? I'm sure it is something simple I am missing, but I just don't see it (output below). Thanks, Sean > readLines(url("http://www.bioconductor.org/biocLite.R")) [1] "source(\"http://bioconductor.org/getBioC.R\")" [2] ""

OK, I really am struggling with this one! Forgive me if I am being stupid.... I am running R 1.7.1 on Suse Linux 8.1. I connect to the internet through a proxy so I have: IAHC-LINUX03:~ # echo $http_proxy wwwcache.bbsrc.ac.uk:8080 IAHC-LINUX03:~ # echo $HTTP_PROXY wwwcache.bbsrc.ac.uk:8080 just in case ;-) SO, i go into R and I get: >

Hi, I am new to using R and Bioconductor. My first attempt at installing R seemed successful. Then while attempting to getBioC() I had to force quit the R application since I had to attend to something else urgently. When i returned and tried to getBioC, I am getting errors indicating that there is a lock on some files. So i would like to uninstall/remove all R components and Bioconductor

I was trying to install R on a unix server. Because of a firewall i can't install biocLite for working with Bioconductor. With windows it wasn't a problem. I used the option '--internet2' to bypass the firewall. I don't have any idea, how to do it with unix. I tried to set my proxy >Sys.putenv("http_proxy"="http...:8080")

Hi Thanks once again for your help, I do appreciate it..... however.... Here is what I get with your test.... (under tcsh - i normally use bash, but I will keep everything the same) users/mwatson> env http_proxy=http://wwwcache.bbsrc.ac.uk:8080/ R >options(internet.info=0) >update.packages() trying URL `http://cran.r-project.org/src/contrib/PACKAGES' unable to connect to

>I just installed bioconductor via getBioC.R but there >is 3 problems: apparently some libraries are missing >and I don't know which one, and even the XML package >add a error message like : >1:Installation of package Rgraphviz had non-zero exit >status in: installPkg(fileName, pkg, pkgVer, type, >lib, repEntry, versForce) >2:Installation of package rhdf5 had non-zero

Hi , there: I used function source to download the package but found > source("http://www.bioconductor.org/getBioC.R") Error in file(file, "r") : unable to open connection In addition: Warning message: unable to resolve 'www.bioconductor.org'. Then I downloaded the packages from CRAN and found > local({a <- CRAN.packages() +

Dear list, I have a lot of troubles installing Rgraphviz. I installed graphviz 2.13 from "graphviz-2.13.20061222.0540.tar" I installed the library Rgraphviz > getBioC("Rgraphviz") Running biocinstall version 2.0.8 with R version 2.5.0 Your version of R requires version 2.0 of Bioconductor. trying URL '

Hi again, I have been playing around with the order of loading packages, and as far as I can tell, there's nothing specific with affycoretools that's causing my Rgui to crash (i.e., shuts down and the Microsoft 'please send error report' box pops up). Instead, it has something to do with the order & type of packages that are loaded that add items to the menu bar by

I would like to use the getBioC.R script from http://www.bioconductor.org/getBioC.R to install the biobase packages. Unfortunately, url() and download.file() die when trying to talk to my proxy: > getBioC("exprs") connect: Cannot assign requested address unable to connect to 'gproxy1.pfizer.com'. connect: Cannot assign requested address unable to connect to

I would like to use the getBioC.R script from http://www.bioconductor.org/getBioC.R to install the biobase packages. Unfortunately, url() and download.file() die when trying to talk to my proxy: > getBioC("exprs") connect: Cannot assign requested address unable to connect to 'gproxy1.pfizer.com'. connect: Cannot assign requested address unable to connect to

Hi Seth, The possibility of caching computations would be a great boon when one is iteratively refining a paper; so I'm most grateful for your work on this. Unfortunately I have a problem to report: ******************installing****************** > source("http://bioconductor.org/biocLite.R") > biocLite("weaver") Running getBioC version 0.1.8 with R version

Hi, I am trying to install Bioconductor software on our server with Red Hat Linux Enterprise (Server) edition version 4, 32GB Ram and automatic proxy configuration (http://www.ntu.edu.sg/proxy.pac) setting. from http://www.bioconductor.org <http://www.bioconductor.org/> website but couldn't install. I encounter the following errors highlighted in RED when I try to download from