similar to: unable to view vignette in R

Hello everyone, I have a problem when loading the library: IlluminaHumanMethylation27k.db I installed the package from zip (from the Bioconductor website), and also installed all the packages it asked for. It went all succesfull: "package 'IlluminaHumanMethylation27k.db' successfully unpacked and MD5 sums checked" But when I am trying to load this library I get an error:

Dear all, I am a PhD student working with Affymetrix HGU133atag array for analyzing the Latin square experiment. I was trying to generate gene expression index for hgu133atag array for PDNN model. While extracting the chiptype specific data structure, I got the following error- > library(affypdnn) Loading required package: affy Loading required package: Biobase Welcome to Bioconductor

Hi, I'm trying to get this library working under R2.10.0. I downloaded it and installed it from zip file. i get the following output. > library(hgu133a2.db) Error in library(hgu133a2.db) : there is no package called 'hgu133a2.db' > utils:::menuInstallLocal() package 'hgu133a2.db' successfully unpacked and MD5 sums checked > library(hgu133a2.db) Loading required

Hi, I am a Ph.D. student from Québec, Canada. I’m a beginner with R and Bioconductor. Until now the only experience I have is in analyzing microarray data using affy and limma packages. Now I am trying to analyze Rat Gene 10 st arrays and I would like to run RMA analysis and Smyth moderated t test on those arrays. Since no cdf official package is available for those arrays, after reading many

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 =

The GeneSetCollection class in the Bioconductor package GSEABase extends 'list' > library(GSEABase) > showClass("GeneSetCollection") Slots: Name: .Data Class: list Extends: Class "list", from data part Class "vector", by class "list", distance 2 Class "AssayData", by class "list", distance 2 If I create

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

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 '

I have developed a problem with the postscript output of plot on Windows. My code still works properly with R 2.3 but, with R 2.4, the white text on red background does not show up. It does, however, show up when output is sent to the screen. Below is my code and sessionInfo. R version 2.4.0 Under development (unstable) (2006-08-29 r39012) i386-pc-mingw32 locale: LC_COLLATE=English_United

I have a simple vector, called tmp that I want to subset based on another vector called vec. Everything works as expected except for below where the subsetting returns something other than the original data. Any ideas? > vec <- c(1,2,3,4,5,59,60,27,32,21) > tmp [1] 1.0 1.1 2.0 2.1 2.2 3.0 3.1 4.0 5.0 5.1 6.0 7.0 8.0 8.1 9.0 [16] 9.1 9.2 10.0 10.1 11.0 12.0 13.0 14.0

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, This is a follow-up to the problem reported here: https://stat.ethz.ch/pipermail/r-devel/2010-September/058460.html After I updated R-2.12 to 2010-09-13 r52905 on the Bioc build system, some of the packages that have a Makefile in <pkg>/inst/doc still don't build on Windows. For example, 'R\bin\R.exe CMD build adSplit' gives: * checking for file

Hi How do I install "gregmisc" packages? I did- % sudo R > install.packages("gregmisc") . . > barplot2() but, Error: couldn't find function "barplot2" -- atuya Mac OSX 10.2.6 R 1.7.1

Hello, I see the following issue in R-devel since 'both' has become the default pkgType for binary platforms. update.packages() fails when you set options(repos). Looks like it is trying to download a tgz file from the src/contrib section of a repository (on a mac). To reproduce this you need to have an older version of AnnotationDbi installed, which I accomplished by faking it,

Dear r-helpers, I am building a package that depends on some others. I recently added a new dependency: package "outliers". But does not work any more. Let me show some information below: carlos at kropotkin:pcrAnalysis$ cat DESCRIPTION Package: pcrAnalysis Type: Package Title: pcrAnalysis Version: 0.7.2 Date: 2007-02-27 Depends: Biobase, methods, outliers Author: Carlos J. Gil

Hi, I discover that when I save a workspace containing a genefilter (pkg from Bioconductor) object I cannot open no more after. I have to restore the .RData file from a backup to be able to start R again. I didn't upgrade to Version 2.2 but I'm not sure that it will solve the problem. Did anyone have encounter the same problem? Below is a short r session to reproduce the error: ...

Hi, I have an RData file containing a GeneSetCollection object (Bioconductor), http://www.cs.mu.oz.au/~gabraham/c2.RData. I think it uses lazy loading because packages are only loaded when I access the object (see below) in the R console. When I try the same with Rscript, it segfaults. This happens on 2.9.0 both on Linux and Mac: Rscript -e 'load("c2.RData"); c2[1]' ***

Running R2.4.0 on Apple Mac OS X 10.4.8, in Emacs ESS mode, and also R.app. In an attempt to learn a bit more about a particular method (geneNames in package affy) I invoked getMethods("geneNames") which produced geneNames methods, but not the one in affy (output below). I had to know the signature (AffyBatch) in order to find the method > getMethod("geneNames",

mogene10stprobeset.db is generated with AnnotationDbi for mouse gene array. I don't find a package that seems generated by AnnotationDbi for exon arrays on the webpage you mentioned. Is it correct? On Tue, Oct 27, 2009 at 7:00 PM, Marc Carlson <mcarlson at fhcrc.org> wrote: > Hi Peng, > > I am not completely clear from your post what you want. ?But most of our > annotation

This is my first post requesting help to this mailing list. I am new to R. My apologies for any breach in posting etiquette. I am new to this language and just learning my way around. I am attempting to run some sample code and and am confused by the error message: Loading required package: rrcov Error in fitNorm2(fdat[, "FSC-H"], fdat[, "SSC-H"], scalefac = ScaleFactor) :