similar to: about image(graphics) function

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

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]

Hi, everyone, I ran the test case in "Introduction to the Bioconductor marrayInput package first. When I ran the session in (read.marrayRaw) I got the following error messages. Other sessions work well. The functions and errors are labled with blue and red respectively. >mraw <- read.Spot(path = datadir, layout = galinfo$layout, gnames = galinfo$gnames, target = swirlTargets) Error

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

Dear all, This message is a kind of 'to be continued...' for that send by /Yu-An Dong,/ [BioC] problems with GO package data <https://stat.ethz.ch/pipermail/bioconductor/2006-February/011760.html>, last february. I've just installed R 2.2.1 on my computer (Windows based version) and downloaded Bioconductor available for this version via the graphical interface facility

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,

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

Greetings! The Bioconductor core group would like to announce the 5th release of Bioconductor, version 1.4. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to upgrade existing tools and check out the new packages. Release 1.4 is intended to be operated with R version 1.9.x, which can be obtained at CRAN

Hi all, I am a relatively new R user... trying to put error bars (from SD values) on my data represented with barplot(). But I can't find any function or instruction to do so. Is there an easier way to do this than using segments() as I saw in an example in the R reference manual ? Then, can I define there graphical apparence ? Thanks for help. Regards Olivier BUHARD [[alternative HTML

Hi all, I know this is a stupid question, but I can't display a text file in a separate console window under a R session in X11 (gnome with MDK 9.2). I use R 2.0.0. When I enter : > file.show("/path/to/my/file/filename.txt" ,pager="gnome-terminal") the new window opens and then I just obtain the blinking cursor after the console prompt :-( I always obtain the same

Dear all, I have some additionale question concerning the spgrass6 package. * When you set a region in GRASS, does the readGRASS6 function in R only load data contained in the zoomed region or the whole map ? * When you have a MASK map in grass, does the readGRASS6 function in R only load data contained inside the MASK area ? Could this be the problem ? Thanks, Jessica

Dear all, Trying to produce 4 maImage plots (marray package) on the same device (2 on the top and 2 on the bottom) with the layout() function or the split.screen() function, we are facing the following problem: it seems that maImage() does nt care about any of these 2 functions, and plots only one image at a time. Maybe this is inherent to this maImage() function, but we did not find anything

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 =

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

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, 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

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

Hi, How can I write the output to an excel (csv) file without printing row names (i.e without breaks). Here is my code: library( fn <- function() { q <- c(1,2,3) write.csv(q,"C:/Temp/op.xls", append = TRUE, row.names = FALSE,quote = FALSE) } # Function Call for(i in 1:3) { fn() } Present Output : x 1 2 3 x 1 2

I'm working on some heatmaps, and the person I'm working with would prefer a red-black-green color palette (red denoting gene induction and green denoting gene repression). Does such a palette exist already? If not, is there an easy way to create one? Thanks, Jake

Dear all, I am finding difficulty in the following, I would like to create an empty matrix e.g. 10x10 of 0s and sequentially fill this matrix with randomly placed a 1s until it is saturated. Producing 100 matrices of sequentially increasing density., This process needs to be randomized 1000 times., I assume i should run this along the following lines, 1) Create 1000 matrices all zeros, 2) add