similar to: repeating colors in graph 2

Using R-1.8.0 (d/l and compiled on 2003-10-01) on WinXP, I seem to be unable to determine the maximum memory allocated to R. The help still says to use memory.limit(size=NA), but this returns the value NA. In addition, I have set --max-mem-size=2G but I run out of memory somewhere around 500Mb (which is why I am trying to find out how much memory is allocated). I don't have any other programs

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

I have a plot with 13 lines and R repeats colors. Is there any way to make R not repeat colors, or is this just a fundamental limitation on R's part to say have only 8 colors that it can use? Anna

I get a segfault when using savePlot("foo","pdf"). FWIW, I don't have a problem using the canonical pdf("foo.pdf") plot(something) dev.off() Best, Jim > R.Version() $platform [1] "i386-pc-mingw32" $arch [1] "i386" $os [1] "mingw32" $system [1] "i386, mingw32" $status [1] "Under development (unstable)"

> R.version.string [1] "R version 2.1.0, 2005-03-17" I don't see anything in either https://svn.r-project.org/R/trunk/NEWS or in the Changes file for R-2.1.0 about changes in package.skeleton() (nor in the help page), but when I run this function, all the .Rd files produced are of the data format even if all I have in my .GlobalEnv are functions. A trivial example is to run the

Hi, I have a package that contains two vignettes that both use saved objects in the examples directory of the package. With previous versions of R I could have a code chunk in the vignette like this: <<echo=false>>= load("../examples/somedata.Rdata") @ followed by a code chunk like <<eval=false>>= foo <- bar("data") @ that simulated the actual

Hi all, In the CHANGES file for R-2.3.0alpha, there is the following statement: winMenuAdd() now has no limits on the number of menus or items, and names are now limited to 500 (not 50) bytes. However, I can reproducibly get a segfault using this (admittedly silly) example: for( i in 1:5) winMenuAdd(paste("Test", letters[i], sep="")) for(i in 1:5) for(j in 1:24)

The function knn.cv in the class package doesn't have error checking to ensure that the length of the classlabel argument is equal to the number of rows in the test set. If the classlabel is short, the result is often a segfault. > library(class) > dat <- matrix(rnorm(1000), nrow=10) > cl <- c(rep(1,5), rep(2,5)) > cl2 <- c(rep(1,5), rep(2,4)) > knn.cv(dat, cl) [1] 2

Hi, I am unable to build a package I maintain using a relatively current build of R-2.4.0 alpha, whereas the package builds just fine on R-2.3.1. Both versions of R were built from source. I'm hoping a guRu might be able to give some help. Some snippets from the build process: R-2.3.1 making DLL ... gcc -Ic:/R-2.3.1/src/extra/zlib -DHAVE_ZLIB -Ic:/R-2.3.1/include -Wall -O2 -c

I just built R-devel from source on OS X (Tiger), using the subversion sources. Running ./tools/rsync-recommended didn't download rcompgen. I checked http://cran.r-project/src/contrib/2.7.0/Recommended and indeed, this package is not there. If I try to install using install.packages I get > install.packages("rcompgen", type="source") --- Please select a CRAN

If one wants to unload compiled code for a package containing a namespace, my understanding is that .onUnload() should be used, with a call to library.dynam.unload(). This is used in e.g., the stats and methods packages, but it appears to me that the compiled code is not being unloaded when the package is detached(). Am I misunderstanding something? Best, Jim > search() [1]

With 2.1 on Windows XP SP2 (32 bit) I also get no title in a png plot, so I can reproduce this bug. R is installed from pre-built binary. No title appears when I run this: png("foo.png") plot(1:10, main = "foo") dev.off() The jpeg device behaves as expected: jpeg("foo.jpg") plot(1:10, main = "foo") dev.off() Thoughts on this?

Hi, I have a data matrix of gene expression data from two groups that I would like to compare using the t-test. The data has been processed using RMA and transformed using log2. I would like to compare the two groups for each gene (N=10,000 genes) and have a result that lists the p-value for each test. Can anyone help me with the t.test setup for this analysis? Thanks, Rich Rich Roth, PhD

Hi everyone, I'm trying to generate an RNA degradation plot of the Estrogen example data plot, but seem to get an error. I've tried defining an ylim value, ylim=c(0,30) , but it doesn't seem to work either. My code is as follows: > RNAdeg<-AffyRNAdeg(Data) > png(DegLoc, width=720, height=720) > par(ann=FALSE) > par(mar=c(3,3,0.1,0.1)) >

I am running R 2.0.0, GOstats 1.1.1 and GO 1.7.0, and when I use the function GOHyperG, I have the following error: w1<-as.list(hgu95av2LOCUSID) w2<-unique(unlist(w1)) set.seed(123) myLL<-sample(w2,100) xx <- GOHyperG(myLL) Error in mget(x, env = GOTERM, ifnotfound = NA) : recursive default argument reference In fact first I tried this function with my locusId ' list (with

Hello does anyone know what algorithm is used to produce the hierarchical clustering in the gplots package using the function heatmap.2? I think it may be the complete linkage clustering algorithm, but I can't find a source that seems reliable. Thank you and sorry if I posted this in the wrong place. If I have, please let me know and I will move it to the appropriate list. -- View this

Can someone throw light on the following problem I am having with RODBC? There's an Excel file I am trying to read from, it has one sheet named 'nameclass'. Thanks in anticipation. Vishal Belsare > library(RODBC) > con = odbcConnectExcel(file.choose()) > tbls <- sqlTables(con) > tbls TABLE_CAT TABLE_SCHEM TABLE_NAME TABLE_TYPE REMARKS 1

All, Anybody can tell how to export a R plot onto Word (or Power Point)? Many thanks in advance. -MY

Hello, I've a question about the fdr method in p.adjust: What is the threshold of the FDR, and is it possible to change this threshold? As I understand the FDR (please correct) it adjusts the p-values so that for less than N% (say the cutoff is 25%) of the alternative hypothesis the Null is in fact true. thanks a lot for help, +regards, Arne

Is there any way to control the format of the axis label numbers on a plot? More specifically, I have some plots that get axes with label numbers in exponential format, and I'd like to change that to non-exponential. Thanks!! -- M. Edward (Ed) Borasky, MS, MNLP, NST, FBG, PGS & PTA znmeb at borasky-research.net http://www.borasky-research.net