similar to: 3 questions: debug R script, multi-level sorts, and multi-gsub

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

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:

Hi, I am using "*Maanova* package" to do anova. I have created *datafile* with probeID as the first column, which is a tab limited text file and also created *designfile*. I have created *readma object* which is named as abf1. >From that readma object, i have to create data object by using *createData*function and also i hav to create model object by using *makemodel* function,

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: ...

I am developing a package that imports some functions from another package. The imported package (qcc) does not have a namespace and this is causing problems with loading of my package, which has a namespace. Is there a workaround to allow loading the namespace-less package? I searched the archives and found a suggestion that the package should be included in the Depends list, but this has not

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

dear all, I have a problem with a masked object in a package we created here. we make a package for a workflow of internal analysis of microarray data. to create the package we used: > install.packages(pkgs="affyAnalysis", repos=NULL) > R CMD INSTALL affyAnalysis Erzeuge Verzeichnisse ... Erzeuge DESCRIPTION ... Erzeuge NAMESPACE ... Erzeuge Read-and-delete-me ... Kopiere

My machine has 8GB memory. I had quit all other programs that might take a lot of memory when I try the script (before I post the first message in this thread). The cdf file is of only 741 MB. It is strange to me to see the error. On Mon, Dec 28, 2009 at 2:38 AM, Wolfgang Huber <whuber at embl.de> wrote: > Dear Peng Yu > > how big is the RAM of your computer? You could try with

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

Dear list, I?m using R embedded in another program (coded in tcl/tk) under Windows Vista. In this context I don?t launch Rgui.exe but rather Rtem.exe. Now I have a problem finding libraries not specifically installed as administrator (and which are not in the path ?program files? but in Contacts\Documents of the current user). To be precise, the user launching my tcl/tk program can?t find

Hello All R-Gurus: ISSUE: Cannot view R vignettes due in Ubuntu Linux (a debian variant). note: this issue has been posted to this list before with no responses given see https://stat.ethz.ch/pipermail/r-help/2007-September/141178.html DETAILS: I am trying to view an R vignette. Here is the situation: I issue the openvignette(), then select the vignette I wish to view...and the system returns:

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, Given test <- matrix(c(0,2,0,1,3,5), 3,2) > test[test>0] [1] 2 1 3 5 These are values >0 > which(test>0) [1] 2 4 5 6 These are array indices of those values >0 > which(apply(test>0, 1, all)) [1] 2 This gives the row whose elements are all >0 I can't seem to get indices of rows containing one or more elements >0 [[alternative HTML version deleted]]

Hello, I work with two packages sna and graph from CRAN resp. Bioconductor. Both packages have a function called "degree". Therefore one of the functions is masked by the other and which one gets called depends on the order of loading. The problem is that both package do not have a namespace, therefore calling the masked function with "package::degree" does not work.

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

Hi, I am using "*Maanova* package" to do anova. I have created *datafile* with probeID as the first column, which is a tab limited text file and also created *designfile*. I have created *readma object* which is named as abf1. >From that readma object, i have to create data object by using *createData*function and also i hav to create model object by using *makemodel* function,

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Hi, How to cbind or rbind different lengths vectors/arrays without repeating the elements of the shorter vectors/arrays ? > cbind(1:2, 1:10) [,1] [,2] [1,] 1 1 [2,] 2 2 [3,] 1 3 [4,] 2 4 [5,] 1 5 [6,] 2 6 [7,] 1 7 [8,] 2 8 [9,] 1 9 [10,] 2 10 [[alternative HTML version deleted]]

Hi, Is there a way to write a table to pdf ? I have checked write.table, it only writes to text file. [[alternative HTML version deleted]]