similar to: Deleting multiple rows from a data matrix based on exp value

Displaying 20 results from an estimated 5000 matches similar to: "Deleting multiple rows from a data matrix based on exp value"

2007 Sep 24
1
Error: cannot allocate vector of size...
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
2008 Mar 08
3
expression matrix
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
2008 Feb 27
2
problem with creation of eSet
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 =
2008 Mar 20
2
Error in function (classes, fdef, mtable): unable to find an inherited method for function "indexProbes", for signature "exprSet", "character"
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
2012 Mar 31
1
basic subset question of matrix
Dear list, I would like to subset a large expression matrix based on rownames. That is, I have a list (as a txt-file) with gene names that matches some of the rows in my matrix. I've loaded my matrix as well as gene list using the read.table() command. myMatrix <- read.table("name_of_file.txt", header=T, row.names=1) list_to_keep <- read.table("name_of_file.txt",
2008 May 30
1
A question about *read.table()*
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
2003 Oct 27
1
initialization of S4 classes/methods
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
2003 Dec 26
1
Problems converting output from Sweave to PDf
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
2006 Oct 12
1
getMethods() not finding all methods
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",
2003 Mar 26
1
formal methods and classes and capitalization conventions
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
2006 Feb 20
1
mva.pairs
Hello, I am using the following code to plot an MVA plot. library(affy) library(Biobase) library(limma) library(gcrma) pd<-read.phenoData("Clk.targets.2.txt",header=TRUE, row.names=1,as.is=TRUE,sep="\t") Data <- ReadAffy(filenames=pData(pd)$FileName,phenoData=pd) Print(Data) eset <- gcrma(Data) write.exprs(eset,
2003 Sep 05
2
S4 Method Collisions with "[" (PR#4075)
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: >
2013 Jan 12
3
heatmap.2 problem
Dear List, I'm trying to generate a simple heatmap that has each row and column separated by a black line. However, for some reason this only happens for the first and last color. The middle color in my colorpanel() command has an addition horizontal and vertical line that I would like to get rid off. Any suggestions? #my code below my.matrix <- cbind(func.1 =
2011 Jun 08
1
R command window
Hello. I'm a visually impaired statistician, working at the National Institute of Public Health in Denmark. I would like to use R for some analysis and have succesfully installed version 2.13.0 on my Windows XP labtop. I then would like to run R interactively but unfortunately the textfont of the command line in the R window is very hard for me to read. I use a special program called
2007 Sep 15
0
Question about VarSelRF
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
2003 May 29
0
Bioconductor 1.2 Released
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
2006 Dec 14
1
[announce] iproute2 2.6.19-061214
This is an update to the iproute2 command set. It can be downloaded from: http://developer.osdl.org/dev/iproute2/download/iproute2-2.6.18-061214.tar.gz Repository: git://git.kernel.org/pub/scm/linux/kernel/git/shemminger/iproute2.git For more info on iproute2 see: http://linux-net.osdl.org/index.php/Iproute2 The version number includes the kernel version to denote what features are
2003 Jul 14
0
Fwd: how to make exprSet
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
2012 Jul 31
4
Long processing time using Augeas
Hi! I using Augeas to handle dump and passno for certain mount points in /etc/fstab. Each mount point is defined as it''s own augeas block: augeas { ''homeLV'': context => ''/files/etc/fstab'', changes => [
2003 Oct 30
0
Release of Bioconductor 1.3
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?