similar to: Help reg Genome view

Hi, While trying to install hgu133acdf- windows package in R im getting the following error and unable to install the same. > source("http://bioconductor.org/biocLite.R") > biocLite("hgu133acdf") Using R version 2.10.0, biocinstall version 2.5.10. Installing Bioconductor version 2.5 packages: [1] "hgu133acdf" Please wait... trying URL '

Hi all , I have one query. i have list of some .cel files. in my program i have to mention the path of these .cel files part of my program is, rna.data<-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) in the place of "datadir" i have to mention the character string of the

Hello All R-Gurus: ISSUE: Cannot view R vignettes due in Ubuntu Linux (a debian variant). note: this issue has been posted to this list before with no responses given see https://stat.ethz.ch/pipermail/r-help/2007-September/141178.html DETAILS: I am trying to view an R vignette. Here is the situation: I issue the openvignette(), then select the vignette I wish to view...and the system returns:

Hello all, I am trying to use "clim.pact" package for my work, but since this is the beginning for me to use gridded datasets in "R", I am having some trouble. I want to do seasonal analyses like trends, anomalies, variograms, EOF and probably kriging too to downscale my 1 degree gridded data to 0.5.  So, as a first step, I compiled my entire dataset (with 25

Hi, I am trying to install GenomeGraphs package from bioconductor, but failed by a non-zero exit error. From the error message, it seems that there is a shared library problem. Any suggestion on fixing it? Thanks so much. > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915

Hello R help list I have been using the smoothScatter function within the "geneplotter" package to make some graphs using a Sweave Rnw script called via Rscript in a DOS/Windows batch file. The Rscript will ultimately be called by a web service with time-out constraints, hence things need to run as swiftly as possible. The geneplotter package is currently loaded each time R is invoked

Hi, I have been trying to plot density plots using the example on: http://addictedtor.free.fr/graphiques/graphcode.php?graph=139 I used to use this function, but I cannot get any old code or even the example to work. library("geneplotter") require("RColorBrewer") x1 <- matrix(rnorm(1e4), ncol=2) x2 <- matrix(rnorm(1e4, mean=3, sd=1.5), ncol=2) x <-

Hi, this is tangentially related to the recent discussion on vignettes. vignette() currently produces a listing of available vignettes, but these are not clickable. Since R has a browseURL() function, it seems natural to have a version that produces HTML with clickable links. Here's an attempt at that: source("http://dsarkar.fhcrc.org/R/vignette-browser.R") browseVignettes()

I downloaded: http://www.bioconductor.org/data/metaData/hgu95av2_1.7.0.tar.gz described as: Package: hgu95av2 Title: A data package containing annotation data for hgu95av2 Version: 1.7.0 Created: Wed Jan 12 16:57:23 2005 Author: Lin,Chenwei Description: Annotation data file for hgu95av2 assembled using data from public data repositories Maintainer:

In ?Sweave, it refers to Sweave User Manual. In the doc folder of utils package, I see "Sweave.pdf". However, I can't find it from within R > vignette("Sweave User Manual") Warning message: vignette ?Sweave User Manual? not found > browseVignettes("utils") No vignettes found by browseVignettes("utils") > library(help=utils) does not

Hello, I am attempting to use smoothScatter to plot a heatmap of locations of events in an x-y axis. When I plot the heatmap without passing xlim and ylim parameters, it fills the plot area but the perspective is a bit skewed. I would like to standardize these plots to a uniform window size that does not depend on the range of values in the dataframe. However, when I resize the plot using xlim or

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 am struggling with an issue related to static vignettes: they work, but only when present in double in the tarball -- in the folder inst/doc and vignettes; see below for details. Details: I am pre-compiling heavy vignettes thanks to the vignette builder R.rsp. So basically, I have PDF files which I want the package to use as Vignettes. For this, I have the following in my

Hi, I'm trying to make a chromosomal map in R by using the locus. I have a list of genes and their locus, and I want to visualise that so you can see if there are multiple genes on a specific place on a chromosome. A example of what I more or less want is below: http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG The genes and locus are here:

Dear list, I have a lot of troubles installing Rgraphviz. I installed graphviz 2.13 from "graphviz-2.13.20061222.0540.tar" I installed the library Rgraphviz > getBioC("Rgraphviz") Running biocinstall version 2.0.8 with R version 2.5.0 Your version of R requires version 2.0 of Bioconductor. trying URL '

Hello, I am searching for the best method to plot two variables with points whose output color depends on the size of a third variable. For example, the darkness of the x-y point would increase incrementally based on the size of the z value, similar to the colramp parameter in geneplotter. This would be analagous to symbols(), except changing the selection from the color gradient rather than the

Dear R users, I like to plot a matrix A which looks like this: ,1 ,2 ,3 ,4 1, 1 10 100 1000 2, 0.5 0.2 1.0 4.3 3, 0.1 0.2 0.3 0.5 ..... where the 1st row is representing the X-axis values. The subsequent rows should be plotted on the y-axis. I would prefer to use the smoothScatter plotting function of the geneplotter package, but to begin with R I'd be happy to use

Hi How do I install "gregmisc" packages? I did- % sudo R > install.packages("gregmisc") . . > barplot2() but, Error: couldn't find function "barplot2" -- atuya Mac OSX 10.2.6 R 1.7.1

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

Hi everybody, I am wondering how i can add a "stretch" color bar / legend to a graph that uses colorBrewer to define the colors in it. I will try to explain my graph, but i also uploaded it at: ftp://ftpext.usgs.gov/pub/er/fl/st.petersburg/Monica_pal/ The file is: robcor_training_pca.pdf - i will also attach this file in case some people accept attachments. So i took apart the