similar to: install "multtest" and "preprocessCore" packages in Bioconductor library

Hi, I am trying to install Bioconductor onto R version 2.7.0 for Windows. I installed R, then followed the instructions on http://www.bioconductor.org/download, which state that you should type the following: source("http://bioconductor.org/biocLite.R") biocLite() When I do that, I get the following error: Running biocinstall version 2.2.9 with R version 2.7.0 Your version of R

Bonjour! Je suis en train de faire un projet utilisant Affymatrix mais j'ai un probl?me ? t?l?charger un package depuis R: une fois que je t?l?charge le package et je demande de faire "rma" ca sort l'erreur suivante et je n'ai aucune id?e de comment je pourrais faire. > library(preprocessCore) > plac.rma <- rma(plac.new) Background correcting Normalizing Calculating

Neither biocLite nor the GUI menus can install packages on my system. Here is relevant output: > version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31) > source("http://bioconductor.org/biocLite.R") BioC_mirror =

To All How does one get a list of functions from a loaded package so that one can then get the appropriate help for each of the functions. Currently my method is based on a lot of trial-and-error. Here's an example of what I mean... >From this forum I learn that an interesting package called "multtest" exists on Bioconductor. I then use R Console's "Packages" --

I always followed http://cran.r-project.org/bin/linux/ubuntu/ to install R on Ubuntu 8.1. I had no errors before! > install.packages("XML") Warning in install.packages("XML") : argument 'lib' is missing: using '/usr/local/lib/R/site-library' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL

Hello! I downloaded a package "multtest" (from bioconductor.org) in R, and installed it by 'R CMD <package>' (after unzipping and taring). The problem is when I say 'library(multtest)' in R, the following error is generated: Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library

I have been running R CMD check for the first time on of our own packages, which otherwise builds, installs and runs just fine. The package depends on package akima and suggests package multtest; suggesting multtest is indicated because a) it loads a lot of other Bioconductor packages, very slowly, and b) it is only needed for one specific subroutine, which executes require(multtest)

Full_Name: Ken Kompass Version: 2.2.0 OS: winXP pro (2002 version, SP2) Submission from: (NULL) (128.252.149.244) Using R2.2.0 I get this error msg when loading certain bioconductor libraries (depending on whether the library contains file named "all.rda" in R folder of library) : > library(multtest) Error in open.connection(con, "rb") : unable to open connection In

Hi, Installing from binaries on Windows: > install.packages("multtest") Warning: dependency 'Biobase' is not available trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.12/multtest_2.6.0.zip' Content type 'application/zip' length 1645590 bytes (1.6 Mb) opened URL downloaded 1.6 Mb package 'multtest' successfully unpacked

Hi, I am using SAM (from siggenes_1.2.11 package) method to select genes from a microarray data set. After installing the latest R2.4.0 on my computer, to my surprise the results are totally different from that calculated using R2.1.1. Even the example code doesn't work the same way under these two versions of R. Does anybody know what is going on? Thanks for any suggestions.

Hi, With recent versions of R-devel, "R CMD check" complains about some "Rd files with unknown sections". hpages at gladstone:~> R CMD check multtest_1.9.4.tar.gz ... ... * checking Rd files ... WARNING Rd files with unknown sections: /home/hpages/multtest.Rcheck/00_pkg_src/multtest/man/boot.resample.Rd: notes

Dear R-help Hi, I'm Won. I try to do microarray normalization by R. I use justRMA function within affy package, got error about segment fault. I don't know why it happen. I attached error below. Please help me. Thank you. Cheers, Won ======================= OS : Redhat linux Cpu : intel xeon X5570 Memory : 26Gb & OS : Ubuntu Cpu : intel q6600 Memory : 8Gb

Hello R experts, I am trying to analyze this dataset and am stuck on this problem for quite some time now. I am using mt.rawp2adjp. the output that came out was a matrix with two colums since I had asked it to calculate the adjusted p values using one method. so it has the two columns as: rawp BH I combined these using cbind with my actual dataframe. checked using head all was fine. thereafter I

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 have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

Hi, R has been built against FlexiBLAS in rawhide [1, 2]. These are the R packages that need to be rebuilt: R-ape-0:5.4-2.fc33.x86_64 R-expm-0:0.999.4-7.fc33.x86_64 R-gee-0:4.13.20-4.fc33.x86_64 R-gss-0:2.2.2-3.fc33.x86_64 R-igraph-0:1.2.5-3.fc33.x86_64 R-msm-0:1.6.8-5.fc33.x86_64 R-preprocessCore-0:1.50.0-4.fc33.x86_64 R-qtl-0:1.46.2-4.fc33.x86_64 R-quadprog-0:1.5.8-5.fc33.x86_64 Could

Hallo, I just installed all needed packages for my project on my PC. But I cannot load all at one time. I now want to load limma. How can I realize the following plan: I want to install for example limma inclusive all needed other sub packages (add-on). Can anyone tell me the corresponding command? Thanks, Corinna Here is the result of the command library(): Pakete in Library

Hi All, I am using normalize.quantiles (package preprocessCore) to process a 8300 row x 96 col matrix, all numerical data. When I limit the input matrix to 8300 x 67, the function works fine and my data is normalized. But when I increase the input matrix size to 8300 x 68, the function processes but instead of giving normalized data, it gives me all the same number. With 96 columns (the whole

Not sure if this is an R or BioC question so will cross-post. I cannot extract R code from vignettes because system.file("doc", "my.bioc.package") returns "". I got this code directly off of http://www.bioconductor.org/docs/vignettes.html. A specific example using siggenes follows but I have tested this using multiple packages, including those for which I can

> From: Thomas Lumley [mailto:tlumley at u.washington.edu] > > Please don't send these messages to r-announce. r-announce is for > announcements. Isn't r-announce supposed to be moderated? I posted to r-announce about a minor update in randomForest and was rejected. I was told that it's meant for new or significant upgrades in packages, etc. Andy