similar to: Error in function (classes, fdef, mtable): unable to find an inherited method for function "indexProbes", for signature "exprSet", "character"

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",

Hello, I am to run this R script but i keep getting this error. > expr<-exprs(golubMerge) Warning message: The exprSet class is deprecated, use ExpressionSet instead I tried to find information on the website but no luck. (exprSet...etc) thank you. -- View this message in context: http://www.nabble.com/expression-matrix-tp15912874p15912874.html Sent from the R help mailing list archive

Hi, I want to change .RDA file to a text file. So I did as follows. >load("my.rda") >ls() ---> then it showed [1] exprs >write.table(exprs,"C:\\my.txt",sep="\t") I was successful with the first .RDA file. Then I used the same commands with another .RDA file (172 MB)which is 4 times bigger than the first file (41.2 MB). When I put the last command

Hi, I am having troubles with creating an eSet and would appreciate any help on the following problem. I am trying to create an eSet using the following code pd <- read.table(file="pdata.txt",header =TRUE,row.names=1); colnames(pd) <- c("type","tumor","time","id"); pdN <- list(type =

Martin Maechler has suggested that I post this comment to r-devel. It was originally posted to bioconductor. --------------------------------- I'd like to raise the issue of a capitalization convention for naming objects in R. Almost everything in R used to be lowercase but recently there is increasing use of mixed upper/lower case to define names. There is potential for using the

Hi list, I have a question about using *read.table()* to read in a txt file. Basically, it consists of 16346 rows, 6 columns (no header). The code I used is: exprSet <- read.table('process_all4_GSA2.txt', row.names = 1,header =FALSE) and I got an error message: > exprSet <- read.table('process_all4_GSA2.txt', row.names = 1,header =FALSE) Error in

An embedded message was scrubbed... From: "Zhongming Yang" <Zhongming.Yang at cchmc.org> Subject: how to make exprSet Date: Mon, 14 Jul 2003 12:16:33 -0400 Size: 683 Url: https://stat.ethz.ch/pipermail/r-help/attachments/20030714/6e4061d3/attachment.mht

I'm seeing weird issues in methods initialization, i.e. loading marrayClasses loads Biobase, and when explicitly done, as in library(Biobase) library(marrayClasses) is fine, but when Biobase is loaded via a require statement in marrayClasses' .First.Lib, I end up with: Warning message: In the method signature for function "coerce", class "exprSet" has no

I am having trouble converting the output from Sweave into a valid PDF file. I have created a simple .Rnw file which will become a full vignette at some point, but during the intermediate testing, I got errors from texi2dvi. This is what I have done. 0) Using a Windows Xp system 1) Created a file called GeneSpring.Rnw 2) Convert this to Tex using Sweave("GeneSpring.Rnw") from within R

Full_Name: Colin A. Smith Version: 1.8.0 OS: Mac OS X 10.2.6 Submission from: (NULL) (216.102.90.18) Both Biobase and my package annaffy use S4 classes to define methods for "[". Both packages use the save image method of installation. (See annaffy 1.0.3 in BioC CVS.) Depending on how both packages are loaded, the Biobase definitions seem to be getting masked out: >

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

Hi! Is There a way to manually create an affybatch object from qPCR array data? -- View this message in context: http://r.789695.n4.nabble.com/Creating-affybatch-objects-from-matrix-data-from-qPCR-array-tp3921559p3921559.html Sent from the R help mailing list archive at Nabble.com.

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="") >

Hi, I have two data set of normalized Affymetrix CEL files, wild type vs Control type.(each set have further three replicates). > wild.fish AffyBatch object size of arrays=712x712 features (10 kb) cdf=Zebrafish (15617 affyids) number of samples=3 number of genes=15617 annotation=zebrafish notes= > Dicer.fish AffyBatch object size of arrays=712x712 features (10 kb) cdf=Zebrafish (15617

Dear List, I have a data matrix that consists of ~4500 rows and 25 columns (i.e. an exprSet object that I converted via the 'exprs' function into a data matrix) Now I want to remove/delete the rows where all exp. values in that particular row are below or equal to a specific cut-off value (e.g 1.11) I have tried using several commands to address this issue: >Matrix[rowSums(Matrix

The Bioconductor core group would like to announce the 1.3 release of the Bioconductor software. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to check them out. Release 1.3 is intended to be operated with R version 1.8.X, which can be obtained at CRAN (http://cran.r-project.org/) -- WHAT FEATURES DOES THIS RELEASE PROVIDE?

The Bioconductor core group would like to announce the 1.3 release of the Bioconductor software. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to check them out. Release 1.3 is intended to be operated with R version 1.8.X, which can be obtained at CRAN (http://cran.r-project.org/) -- WHAT FEATURES DOES THIS RELEASE PROVIDE?

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, Reading help("Documentation"), I'm led to believe that a help call like: ?myFun(x, sqrt(wt)) Will search for help on the appropriate method in the case that myFun is generic. This isn't working for me. Here is an example using the Biobase package: ## If Biobase is not installed source("http://bioconductor.org/biocLite.R") biocLite("Biobase")

Dear R-helpers & bioconductor Sorry for cross-posting, this concerns R-programming stuff applied on Bioconductor context. Also sorry for this long message, I try to be complete in my request. I am trying to write a subset method for a specific class (ExpressionSet from Bioconductor) allowing selection more flexible than "[" method . The schema I am thinking for is the following: