[R] png support in R on linux

Hi there, I am sure this question has been posted a couple times before but I could not find a good solution on the web. Is there any way to get png() support in R on SUSE linux? We want to run GenePattern on that server and some workflows use R scripts plotting into pngs. Best wishes Kristia

Re: [R] loss of information in pdf plots

ot dev.off() works precisely, just zoom in far enough so that your screen is able to display the gaps, e.g. by zooming in by 6400% Uwe Ligges On 17.04.2012 15:53, Unger, Kristian, Dr. wrote: Thanks Uwe. Please use the following below to reproduce the problem. Also, find the plots as I get

Re: [R] loss of information in pdf plots

netik / Research Unit of Radiation Cytogenetics Tel.: +49-89-3187-3515 Am 17.04.2012 um 14:47 schrieb Uwe Ligges: On 17.04.2012 14:35, Unger, Kristian, Dr. wrote: Thanks Petr. Unfortunately this does not help. In that case, we need a reproducible example. Uwe Ligges Kristian Am 17.04.2

Re: [R] loss of information in pdf plots

Thanks Petr. Unfortunately this does not help. Kristian Am 17.04.2012 um 14:18 schrieb Petr PIKAL: > Hi > >> >> Hi there >> >> is it possible that pdfs generated using the pdf() function with default > >> settings leads to loss of information? I was plotting copy number > changes >> from Agilent

[R] loss of information in pdf plots

Hi there is it possible that pdfs generated using the pdf() function with default settings leads to loss of information? I was plotting copy number changes from Agilent 180k data in form of rectangles (rect()) while each rectangle represents one region of copy number change. When plotting into

Re: [R] Rmpi installation

ld be >printed, but > an executable named "mtest" should have been produced, which could then > be run typing ./mtest. If the link process failed, then the openmpi >installation was > inconsistent. > >Kind regards > >Hugo > >On Wednesday 15 June 2011 17:45:4

Re: [R] Rmpi installation

id this. On successful completion, no message should be >printed, but > an executable named "mtest" should have been produced, which could then > be run typing ./mtest. If the link process failed, then the openmpi >installation was > inconsistent. > >Kind r

Re: [R] Rmpi installation

does >the link phase succeed? Compile & link using > >$ mpicc mtest.c -o mtest > >Presumably you have already tried to run install.packages("Rmpi"). > > >Kind regards > >Hugo > > > >On Wednesday 15 June 2011 16:22:07 Unger,

Re: [R] Rmpi installation

OPENMPI -I/usr/local/include-fpic -O3 -pipe -march=core2 - >mtune=core2 -ggdb -c internal.c -o internal.o >x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -Wl,--as-needed -o >Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib64/openmpi >-lmpi >-L/usr/lib64/R/lib -lR >

Re: [R] Rmpi installation

D INSTALL >--configure-args="--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include >--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 -- >with-Rmpi-type=OPENMPI" Rmpi_0.5-4.tar.gz > >Best > > > >On Wednesday 15 June 2011 14:25:46 Unger, Kristian, Dr. wrote:

[R] Rmpi installation

Hi there I am trying to install Rmpi (version 0.5-4) on our 8-core SUSE Linux Enterprise Server 11 SP1. I read all I could find about Rmpi installation but still cannot get it working. Here the last command that I used: R CMD INSTALL --configure.args="--with-Rmpi-include=/usr/lib64/mpi/gcc/openm

Re: [R] snow package

Arbeitsgruppenleiter Integrative Biologie / Head of Integrative Biology Group Abteilung für Strahlenzytogenetik / Research Unit of Radiation Cytogenetics Tel.: +49-89-3187-3515 Mob.: +49-160-90641879 Am 12.06.11 18:05 schrieb "Prof Brian Ripley" unter : >On Sun, 12 Jun 2011, Unger, Kristi

[R] snow package

Hi I try parallelising some code using the snow package and the following lines: cl <- makeSOCKcluster(8) pfunc <- function (x) (if(x <= (-th)) 1 else 0) ###correlation coefficient clusterExport(cl,c("pfunc","th")) cor.c.f <- parApply(cl,tms,c(1,2),FUN=pfunc) The parApply results in the error m

[R] correlatation matrix

Hi there, I wonder if there is a way of efficiently generating a correlation matrix of two expression matrices. I want to correlate miRNA and mRNA expression and used the following code: ##dat.mi miRNA expression matrix, dat.m mRNA expression matrix nc <- nrow(dat.mi) cor.mat <- data.frame(rep(N

[R] affymetrix human gene 1.0 st gene level

Hi there I recently got some affymetrix human gene 1.0 st array. I only get out the probe level data and I wonder if there is a function that is able to average the probe level data for each gene? Best wishes Kristian Unger Helmholtz Zentrum M?nchen Deutsches

Re: [R] R console Mac

Thanks Isa. I will post my request to the list that you suggest. Best wishes Kristian Sent from my HTC - Reply message - From: "Ista Zahn" Date: Wed, Mar 9, 2011 22:49 Subject: [R] R console Mac To: "Unger, Kristian, Dr." Cc: "r-help@r-project.org" Hi,

[R] R console Mac

Hi there, I recently switched to Mac and I wonder if there is any way to get the R console to autocomplete names of list objects or slots of objects. The command line version allows to type e.g. list$ and two times the tab button and then comes up with the names of the list objects. Same for slots

Re: [R] survval analysis microarray expression data

Dear Terry thank you very much for this. The number of events in my data is well above the suggested size. What concerns me is the fact that a very high proportion of probes comes up as significant when I just randomly select them. This just seems not be biologically meaningful. Do you know of

[R] survival analysis microarray expression data

Hi there I want to test the expression of a subset of genes for correlation with patient survival. I found out that the coxph function is appropriate for doing this since it works with continuous variables such as Affy mRNA expression values. I applied the following code: cp <- coxph(Surv(t.r

[R] select affy probes of cancer-related genes

Hi! I would like to select probes (affy expression set) of genes that are "cancer-related". Conventionally the decision whether a gene is cancer-related or not is made by looking up the literature. Since this is not possible for all genes on the array I wonder if there is a way of doing this

[R] select affy probes of cancer-related genes

Hi! I would like to select probes (affy expression set) of genes that are "cancer-related". Conventionally the decision whether a gene is cancer-related or not is made by looking up the literature. Since this is not possible for all genes on the array I wonder if there is a way of doing this

[R] manual update Agilent oligo probes

Hi there! I wonder if anybody has some script for updating the annotations of Agilent custom probes. I want to update the annotation file of a custom 180k array. Best wishes Kristian _ Kristian Unger Imperial College London __ R-help@r-pro

Re: [R] Sweve/cacheSweave

, Kristian Cc: 'r-help@r-project.org' Subject: Re: [R] Sweve/cacheSweave On 11/02/2010 6:06 AM, Duncan Murdoch wrote: > Unger, Kristian wrote: >> Hi there >> >> I have a problem with using Sweave in combination with the option driver = >> cacheSweave. >> >>

[R] Sweve/cacheSweave

Hi there I have a problem with using Sweave in combination with the option driver = cacheSweave. Whichever code I try to run - when it comes to converting the tex file into pdf it comes up with the same errors (\csname \endcsname errors). Does anybody have an idea what it going wrong? > Swea