similar to: externals controls normalization

dear all, I try to update my Rversion fro 1.7.1 to 1.8.1 on linux. I have a problem when I try to install pacakges from Bioconductors with : source("http://www.bioconductor.org/getBioC.R") and getBioC(relLevel="release") somme errors append and when I make a library(affy) for example I obtain : > library(affy) Error in setIs("character",

Hi there, I would like to draw a scatter plot and fit a smooth line by loess. Below is the data. However, the curve line started from 0, which my "resid" list doesn't consist of 0 value. It returned some warnings which I don't know if this is the reason affecting such problem. Here I also attached the warning messages. Please let me know if there is a solution to fix this. Thank

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 R developers! Considering I got no response or comments in the general r-help forum so far, perhaps my question is actually better suited for this list? I have added some more hopefully relevant technical details to my original post (edited below). Any comments gratefully received! Best regards, David Kreil. ---------- Dear R experts, I have a problem that is a related to the question

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

How do you update R on Windows and how do you install your own package with windows interface ? regards, Ghislaine GUIGON Biostatisticienne Plate-forme 2 Puces a ADN INSTITUT PASTEUR 25-28 rue du Dr ROUX 75724 Paris cedex 15 FRANCE tel: (33) (0)1 40 61 86 51 fax: (33) (0)1 45 68 84 06

Dear Sir/Madam, I could succesfully normalise my microarray data using marrayNorm package. However, i have not been able to get normalised red and green channel intensities through R package. Is there a possibility to write a formula to calculate back the red and green channel intensities after normalisation of the data. Do I need to incorporate this formula in my R script? I am biologist

I'm updating the loess routines to allow for, among other things, arbitrary local polynomial degree and number of predictors. For now, I've given the updated package its own namespace. The trouble is, panel.loess still calls the original code in package:stats instead of the new loess package, regardless of whether package:loess or package:lattice comes first in the search list. If I

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

Hello, I found a little BUG in loess <stats>. It does not receive the iterations parameter. It can be debugged in the following way: THIS IS AN EXCERPT FROM THE CODE: .... fit <- simpleLoess(y, x, w, span, degree, parametric, drop.square, normalize, control$statistics, control$surface, control$cell, iterations, control$trace.hat) Replace argument iterations with

I'm trying to install packages on windows XP and I have trouble with command Rcmd build (R version 1.8.1) : In the Windows console for package maanova for example, answer is : C:\Documents and Settings\dillies\Mes documents\ghis\packages>Rcmd build maanova * checking for file 'maanova/DESCRIPTION' ... OK * preparing 'maanova': * cleaning src *

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?

Hello, I'm a french student working on a project concerning cDNA microarray. I've chosen to work with R and use the marrayClasses, marrayInput (...) packages. First, when I enter "library(marrayInput)", R warns me about a missing package called "utils" but I can't find it anywhere. Normally this package is installed when you install "base" package.

Dear all, I need some help on matrix design and B statistics by using limma package. I want to compare gene expression in 2 groups of cDNA samples. The experiment compares 4 treated mice(#1,#2,#3,#4) and 4 control mice (#5,#6,#7,#8). The target file is FileName Cy3 Cy5 mice1.spot Control_#5 Treat_#1 mice2.spot Treat_#1 Control_#5 mice3.spot Control_#6 Treat_#2

I noticed a problem using R 2.7.1 on Windows XP SP2 with the precompiled Atlas Rblas.dll. Running the code below causes R to crash. I started R using Rgui --vanilla and am using the precompiled Atlas Rblas.dll from cran.fhcrc.org dated 17-Jul-2007 05:04 for Core2 Duo. The code that causes the crash: x <- rnorm(100) y <- rnorm(100) z <- rnorm(100) loess(z ~ x * y) loess(z ~ x) does

A significant update to the Hmisc package is now available on CRAN for all platforms. Hmisc source is now on github at https://github.com/harrelfe/Hmisc and the full change log may be found at https://github.com/harrelfe/Hmisc/commits/master The most important updates are additions of new graphics functions for summarizing and displaying data with an aim of replacing tables. There is also

Please do as we ask (repeatedly) and study the help page before posting. 'family' is a separate argument, not part of loess.control, as the help page correctly documents. If you use cars.lo2 <- loess(dist ~ speed, cars, family = "symmetric", control = loess.control(surface = "direct", iterations = 20)) cars.lo2$pars$iterations it prints *20*, as it is

Dear List, Having had my appetite sufficiently whetted by Prof. Ripley's email about the new graphics capabilities in Unixes, I wanted to try them out. I updated to svn r44608, configured with the following options: R is now configured for x86_64-unknown-linux-gnu Source directory: .. Installation directory: /usr/local C compiler: gcc -O3 -g -std=gnu99

Dear R experts, I have a problem that is a related to the question raised in this earlier post https://stat.ethz.ch/pipermail/r-help/2007-January/124064.html My situation is different in that I have only 2 predictors (coordinates x,y) for local regression but a number of global ("parametric") offsets that I need to consider. Essentially, I have a spatial distortion overlaid over a