similar to: maImage() and layout()

Dear all, I have a problem with the "subset()" function. I spent all day yesterday with a collegue to solve it and we did not find a satisfying solution (even in the archived mails), so I ask for your help. Let's say (for a simple example) a matrix mat: R> mat cola colb colc [1,] 1 4 7 [2,] 2 5 8 [3,] 3 6 9 My goal is to select the lines of the matrix on the basis of the

Dear all, I just upgraded version of R to R 2.2.0, and I have a problem with a script that did not happen with my previous version. Here is the error : ----------------------------------------- > param<-read.table(file="param.dat",sep ="\t",header=TRUE,fill=TRUE, na.strings="NA") Erreur dans read.table.default(file = "param.dat", sep =

I think I must be missing something obvious, but I'm having trouble getting a data transformation to work on groupings of data within a data frame (csss3) as defined by 2 factors (population, locid). The data are sorted by year within locid within population and I want to lag another variable (dbc), i.e, shift them down by 1 row replacing the first row with NA, within groups defined by

The inst/doc directory of the DAAG package has 6 files coral551.spot, ... that are around 0.85 MB each. It would be useful to be able to zip then, but that as matters stand interferes with the use of the Sweave file that uses them to demonstrate input of expression array data that is in the "spot" format. They do not automatically get unzipped when required. I have checked that

Sorry I put there the ref. : I am using R Version 2.0.1 on a Debian. Florence. ---------- Forwarded message ---------- From: Florence Combes <fcombes@gmail.com> Date: Oct 28, 2005 2:48 PM Subject: multiple graphs in the same ps file ? To: r-help@stat.math.ethz.ch Dear all, I would like to be able to store multiple graphs in one ps or pdf file, but I cannot achieve this only if I don't

Dear all, [I work with a Windows XP Prof. installation, and the 2.0.0 R version] I need to use the aws package, but I have the following error message: > require(aws) Loading required package: aws Error in firstlib(which.lib.loc, package) : couldn't find function "lazyLoad" [1] FALSE I download the .zip file (for Windows) today on the CRAN site, so I think I have

In my package, I create a new method for plot with the following signature: setMethod("plot", signature(x="marrayNorm", y="formula"), plot.ma) where marrayNorm is a class defined in the marray package. After building and installing my package, I get the following warnings when I load my package (with library(maVis)): Warning messages: 1: In the method signature

Dear all, We are facing this problem for long, and so ask for your help. We are plotting 2 graphs in a postscript device (left part -layout function-), and the common legend for these graphs on the right part. The legend in the postscript device looks ok: this is color lines with numbers on the right (6 columns) , see the code below: > nblock<-c(1:48) > leg<-paste(c(1:npin),"

Dear R users, I'am using marray and Limma packages to analyze genepix output. 1) how can I filter bad spots from my data (data contains 3 types of bad spots). my experiment contains 12 samples and the bad spot are not associated to the same probes 2) how can I remove control probes from my data ? I'm sorry, i'm new with R and I can't find answer in packages doc. best regards,

Dear all, I would like to be able to store multiple graphs in one ps or pdf file, but I cannot achieve this only if I don't shut the "postscript" device between the graphs. here is what I managed to do : > postscript(file="test_graph.eps", onefile=TRUE) > plot(1:10) > plot(1:20) > > dev.off()

Hi I want to do something which seems straightforward, but I couldn't find the way to do this. I have a matrix called m for example, and a vector of values (let's call ind this vector) which are indices of lines I don't want to keep. for example I have: > m v1 v2 v3 [1,] 1 4 7 [2,] 2 5 8 [3,] 3 6 9 [4,] 10 11 12 > ind [1] 2 4 I would like to obtain this: > m2 v1 v2

Dear R-helpers, I am running well Perl and R on my Debian Linux, and I tried RSPerl. Installation is ok and all simple functions run well. But I have a problem to call the "lines" function. I would like to draw an histogram with the density curve on. Is is OK in R with the command: >x<-rnorm(1000) >hist(x,prob=T) >lines(density(x)) for example. Now, I have a Perl script

Neither biocLite nor the GUI menus can install packages on my system. Here is relevant output: > version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31) > source("http://bioconductor.org/biocLite.R") BioC_mirror =

Dear all, I try for long to understand exactly what is the factor type and especially how it works, but it seems too difficult for me.... I read paragraphs about it, and I understand quite well what it is (I think) but I still can't figure how to deal with. Especially these 2 mysteries (for me) : 1st when I make a dataframe (with the as.data.frame() or the data.frame() commands) from

Hello, I am interested in performing a 2D loess smooth on microarray data, i.e. log2 ratios on a 2D grid, using different spans in the horizontal and vertical directions (the immediate reason being that replicate spots are laid out in the horizontal direction). Is it possible to do this in R? Functions like loess(stats) seem to apply the same span for all predictors, which carries over to

Hi all, is it possible to modify the way a graph obtained through image(graphics) is filled, I mean starting filling the graphical matrix by row from the upper-left rather than by the lower-left cell... In many cases, it can be usefull to have a representation of the data spatialy corresponding to a real support, as it is the case with the function image(marray) from Bioconductor packages, which

Hi, I am wirting a R script to process some data routinely and have a problem when try to get the content of object in ls()? Here is the script: > ls() [1] "a" "b" [3] "files.num" "fll92_1a_gpr" [5] "fll92_1a_gpr_norm" "fll92_1a.gpr.norm.scale" [7] "fname" "fullnames" [9] "gal" "galfile" [11]

Hello R-Users! I'm using a heatmap to visualize a matrix of values between -1 and 3. How can I set the colors so that white is zero, below zero is blue of increasing intensity towards -1 and above zero is red of increasing intensity towards red? I tried like this (using the marray and gplots packages from bioconductor): mcol <- maPalette(low="blue", mid="white",

Hi Everyone, I have been trying to read some Arrayvision files( 2 channel cDNA) and am having some problem. My code is : setwd('C:/work/data/limma/ndd1'); files <- c('ndd1_1.txt','ndd1_2.txt','ndd1_3.txt'); RG=read.maimages(files,"arrayvision",sep="\t"); #Normalisation MA=normalizeWithinArrays(RG); #plotPrintTipLoess(MA); #Fit Linear

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