similar to: Bioconductor 1.2 Released

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?

The Bioconductor development team announces release 1.1 of the Bioconductor packages for the analysis of genomic data. Bioconductor is an open source bioinformatics software project based on R. Version 1.1 features: ===================== * All packages from the 1.0 release are included. All current bug fixes have been applied, and most have upgraded and provide enhanced functionality. *

The Bioconductor development team announces release 1.1 of the Bioconductor packages for the analysis of genomic data. Bioconductor is an open source bioinformatics software project based on R. Version 1.1 features: ===================== * All packages from the 1.0 release are included. All current bug fixes have been applied, and most have upgraded and provide enhanced functionality. *

Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the genomic coordinates. Furthermore I have no clue how to deal with the fact, that most genes have

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

Hello Everyone, I am writing programs in R from 7 months and I am able to solve most of the errors/issues except for this current post. My Task is to read a Microsoft Excel file(textE_to_affy.csv) which contains the Microarray Expression Values collected from the Illumina Microarray experiment. These collected intensity values need to be normalized(Rank Invariant Normalization) by using the R

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

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

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",

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

Hello sir: As to the "variance stabilization" method which is applied in the "vsn"package under R environment,here's a question about the ratio of the 2 channels: After applying vsn,we can get new_cy5 and new_cy3 intensity according to the original cy5 and cy3 intensity respectively. And the new_cy5 new_cy3 are similar with ln(intensity). But how can I calculate the

Hallo everybody. I want to build my own GO package using the function GOPkgBuilder of AnnBuilder. It uses AnnBuilderSourceUrls to collect data from different ftp sites. These data are not complete for my organism, so I would like to change the ftp adresses to a local one. The changing itself is working but when I run the script I get the following Error: Error in

I would like to announce that my DataLoad utility which can be found at: http://www.vsn-intl.com/genstat/downloads/datald.htm has been updated to support R data.frames. DataLoad reads a large variety of data formats (listed on the web page) and can convert these to ASCII or XDR data.frames. Only the Windows and Linux versions are up to date due to the fact that I no longer has access to a Unix

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

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

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

Dear list members, I am analyzing Affymentrix gene expression data and would like to apply the R package, VarSelRF to identifying small sets of genes that could be used for diagnostic purpose. Basically, the data matrix is composed of 22277 rows (genes) and 65 columns (samples). I did unsupervised clustering using pvclust to get 4 classes. What I would like to do is to get unique genes for each

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 =

Hi there. I got some Problems building an Annotation-Package with AnnBuilder. Not using the function ABPkgBuilder(), but just parts of it to create a package without connecting to the servers, I managed to create a Package, but it seems to be empty. R recognizes it as a package, but is unable to load it. The form of the data is in a correct form, I got an example-annotation-file the function