similar to: Fwd: how to make exprSet

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

R Users: How can I catch R errors and depend on this error call other R functions in Perl? The foolowing is the error message when I use perl call R. Error in nls(modout ~ exp(-b1 * modin)/(b2 + b3 * modin), trace = F, start = c(b1 = 0.005, : singular gradient Segmentation fault Thanks, Zhongming

Dear All: I need draw some figure through trellis.device and save them as pdf files. How can I close trellis.device (something like dev.off() in nonlattice figure)? Many thanks Zhongming Yang --------------------------------- [[alternative HTML version deleted]]

The Bioconductor development team announces release 1.2 of the Bioconductor packages for the analysis of genomic data. Bioconductor is an open source bioinformatics software project based on the R language. Version 1.2 features: ===================== * All packages from the 1.1 release are included. All current bug fixes have been applied, and most have been upgraded and provide enhanced

Hi, I use lm or loess to make smoothing. After smoothing I need "Residual Standard Error" in my script. Could you please tell me how can I get this information? Thanks,

Dear All: In the attached file, I have 3 group patients, and there are 5 in each group (the groups are decided by the prefix of the idno). I want draw a repeat measurement comparison figure. My goal is to list 5 patients from same group on one horizontal line. But xyplot sounds pick them randomly (or I was confused?). Could you please help me modify the following code to accomplish this?

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",

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 trying to use piecewise linear regression to approximate a nonlinear function. Actually, I don't know how many linear functions I need, therefore, I want build an array of regression models to automate the approximation job. Could you please give me any clue? Attached is ongoing code: rawData = scan("c:/zyang/mass/data/A01/1.PRN", what=list(numeric(),numeric())); len =

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

Dear All: Could you please tell me how I can draw figure formatted like figure 4.18 of MASS (4th) with the attached data set? Thanks Zhongming Yang --------------------------------- -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: sample.txt Url: https://stat.ethz.ch/pipermail/r-help/attachments/20050316/abfdb85e/sample.txt

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 =

-------------- next part -------------- An embedded message was scrubbed... From: Shigeki Misawa <misawa at bnl.gov> Subject: Re: Problem with keygen on Solaris 8 system. Date: Mon, 30 Apr 2001 23:59:00 -0400 (EDT) Size: 3533 Url: http://lists.mindrot.org/pipermail/openssh-unix-dev/attachments/20010501/a092310c/attachment.mht -------------- next part -------------- An embedded message was

-------------- next part -------------- An embedded message was scrubbed... From: Omayle.Rondon at movilnet.com.ve Subject: sftp Date: Tue, 5 Aug 2003 18:01:47 -0400 Size: 3494 Url: http://lists.mindrot.org/pipermail/openssh-unix-dev/attachments/20030806/50dbdc11/attachment.mht -------------- next part -------------- An embedded message was scrubbed... From: Omayle.Rondon at movilnet.com.ve