similar to: Question about VarSelRF

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

Dear list, I need to read a big txt file (around 130Mb; 23800 rows and 49 columns) for downstream clustering analysis. I first used "Tumor <- read.table("Tumor.txt",header = TRUE,sep = "\t")" but it took a long time and failed. However, it had no problem if I just put data of 3 columns. Is there any way which can load this big file? Thanks for any suggestions!

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

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, 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

Dear List, I have another question to bother you about how to do clustering. My data consists of 49 columns (49 variables) and 238804 rows. I would like to do hierarchical clustering (unsupervised clustering and PCA). So far I tried pvclust (www.is.titech.ac.jp/~shimo/prog/*pvclust* /) but I always had the problem like for R like "cannot allocate the memory". I am curious about what

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 migrated to a new version of the voip connection vs1 server software and I am now getting these errors when I try to call my voicemail. Any thoughts? The files are there, so I don't get it. Oct 11 19:57:26 WARNING[6587]: format_wav.c:140 check_header: Not a wav file 49 Oct 11 19:57:26 WARNING[6587]: file.c:418 ast_filehelper: Unable to open fd on

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

Hi, You should also check my msc.features.select from caMassClass package. It has feature selection algorithm that I found useful in case of mass-spectra data. It performs individual feature selection and/or removes highly correlated neighbor features. Jarek -----Original Message----- From: r-help-bounces at stat.math.ethz.ch [mailto:r-help-bounces at stat.math.ethz.ch] Sent: Friday, January

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, I have a question: What are the limitations of routing between several IP addresses belonging to one interface? I have a box with one network interface, configured to three different IP addresses. It looks something like this: eth0 xxx.xxx.xxx.11 eth0:01 xxx.xxx.xxx.12 eth0:02 xxx.xxx.xxx.13 What I would like to do is allow eth0''s address to accept and open connections to any

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

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

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, Please consider the example below. How can I manage to overlay the points the way I want in the second case? Thanks, Joh library(ggplot2) # Modify data to match "real" case myDiamonds <- diamonds myDiamonds[["clarity"]] <- as.character(myDiamonds[["clarity"]]) myDiamonds[myDiamonds[["clarity"]]=="I1","clarity"] <- 1

I apologize if this post is not relevant to this mailing list, but I feel it might be of interest for many of you and did not find any other more suitable R-list. We are seeking for a couple of post-docs at University of Ferrara, Italy. The posts are in microarrays data mining and are for people with a degree in Statistics, IT or related. A documented interest in biological problems,

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 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