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Dear R users,  I hope you can help me as you have done before.  I was wondering if I can make some of the points on my graph a different colour and symbol? Some of my soil samples are enriched and I wanted them to be shown with a red triangle and the samples which are not enriched I wanted to show with a blue square. I can't seem to find a way of doing this if there is a way?  My script:  

Hi, I used GOstats to perform enrichment test on a set of genes (20). There are 7 GO terms with pvalue less than cuttoff and therefore shown in the result table. How can I get the information that which gene in the input gene set belong to which GO term of these enriched GO terms? Thanks for any comments. best, Tim [[alternative HTML version deleted]]

I'd like to pick every imbricated five character long subsets from a vector. I guess there is some efficient way to do this without loops... Here is a for-loop-version and a model for output: VECTOR=c(1,4,2,6,5,0,11,10,4,3,6,8,6); ADDRESSES=c(); for(i in 1:(length(VECTOR)-4)){ ADDRESSES[i]=paste(VECTOR[i:(i+4)],collapse="") } > ADDRESSES [1] "14265"

I am trying to use the levelplot function from a command file. Here is the code: library(sp) library(gstat) library(lattice) gatherData <- read.table("~/gather.txt", header = TRUE) grd = makegrid(gatherData$x, gatherData$y, cell.size = 5) k <- krige(z~x+y, ~x+y, data = gatherData, newdata = grd, nmax = 5) levelplot(var1.pred~x+y, k, aspect = mapasp(k), main = "Predicted

What am I doing wrong? > install.packages("Hmisc") trying URL `http://cran.r-project.org/src/contrib/PACKAGES' Content type `text/plain; charset=iso-8859-1' length 47565 bytes opened URL ================================================== downloaded 46Kb trying URL `http://cran.r-project.org/src/contrib/Hmisc_3.0-1.tar.gz' Content type `application/x-tar' length

I am trying to restart on R after 2 months stop. Start with previously functioning procedure: "ch<-odbcConnect("dBase Files")" get "Warning message: ODBC connection failed in: odbcConnect("dBase Files") " I have tried unsuccessfully different working directories. The only change I see is that I am working with a new login account on the same machine.

A disturbing behaviour of R: an import of data using RODBC library (Windows 98, R 1.1.1) recognizes accented characters in variables names but these can't be manipulated further. See below: > library(Rodbc) > ch<-odbcConnect("Paradox Files") > pollut<-sqlFetch(ch,Pollutio) > pollut Mortalit? Densit? Pollution 1 82 600 110 2 97 960

Hello I am getting memory allocation errors when running a function that uses locfit within a for loop. After 25 or so loops, it gives this error. "Error: cannot allocate vector of size 281250 Kb" Running on linux cluster with a Gb of RAM. Problem never happens on my OS X (less memory). The total data is 130 cols by 5000 rows The first 129 cols are response variables, the 130th

Dear r-help reader, I have some problems with the aggregate function. My datframe looks like >frame Day Time V1 V2 1 M 0 3 NA 2 M 0 4 NA 3 M 0 5 2 4 M 1 NA 4 5 M 1 10 6 6 T 0 4 45 7 T 1 4 3 8 T 1 3 2 9 T 1 6 1 I used the aggegate function to obtain the mean in V1 and V2 over the grouping variable Time and Day

When I call an extension (say my extension 1000)and it goes directly to voicemail the first time, it does exactly what it should do (plays announcement and then records, the second time when i call back (within about a minute), it goes directly to a beep (for recording), no announcement. Another thing, during this time when I call 0 (my voicemail access number) it gives me a fast busy. any

Hi, Has anyone written code for isotonic regression on ordered rectangular grids? Nathan Nathan Leon Pace, MD, MStat University of Utah Salt Lake City, UT 84132 Office: 801.581.6393 Fax: 801.581.4367 Cell: 801.558.3987 Pager: 801.291.9019 Home: 801.467.2925 [[alternative text/enriched version deleted]]

R for Mac Special Interest Group Alog with the forthcoming version 1.2.3 of R a new mailing list has been activated. The list is intended to exchange ideas, impressions, give suggestions etc on the portings of R for MacOS and MacOS X. You can subscribe to the list going to its official page: Go to the list page : http://www.stat.math.ethz.ch/mailman/listinfo/r-sig-mac To post a message to

Hi, I am using 2 times series and I want to carry out a regression of Seri1 by Serie2 using structured (autocorrelated) errors. (Equivalent to the autoreg function in SAS) I found the function gls (package nlme) and I made: gls_mens<-gls(mening_s_des~dataATB, correlation = corAR1()) My problem is that I don’t want a AR(1) structure but ARMA(n,p) but the execution fails :

Some naive questions: 1) How to remove a column in a data frame? I expected that rm would work but this is not the case (e.g. rm(dat$yyy) gives Warning message: remove: variable dat$yyy was not found). I only found to assign NULL value (e.g.: dat$yyy<-NULL). Is it the right way? 2) Is the place formerly occupied by dat$yyy automatically gained by R for other uses? 3) If t1 and t2 are 2 only

I want to get subsets averaged on numeric variables number 5:13 but I get the error below that I cannot understand. > is.factor(dat$Statut) [1] TRUE > s<-ave(dat[,5:13],dat$Statut) Error in [<-.data.frame(*tmp*, , value = if (n) { : Argument "i" is missing, with no default Thanks in advance --------------- Charles RAUX, Laboratoire d'Economie des Transports

I use hierclust (hierarchical clustering) in multiv package. In the documentation it is said that plclust (plotting a dendrogram) is available in S-plus. Can I find it anywhere (I have searched through http://lib.stat.cmu.edu/S and found only quotations of plclust in multiv) or is it only part of the S package (which I don't have)? Thanks --------------- Charles RAUX, Laboratoire

Hello, I am trying to place a legend in the title area of a plot. I can not seem to find a way to get legend() to do this. Nor can I use the title() function. Does anyone know a way to do this? I would greatly appreciate any advice. Thanks Josue Samayoa Center for Biomolecular Science & Engineering School of Engineering Division of Physical & Biological Sciences University of

Ok I warned you that I'd been drinking! What I really meant was something to go from: [,1] [,2] [1,] 1 2 [2,] 4 3 to [,1] [,2] [1,] 4 1 [2,] 3 2 to [,1] [,2] [1,] 3 4 [2,] 2 1 to [,1] [,2] [1,] 2 3 [2,] 1 4 Sorry for being a muppet, B Begin forwarded message: > From: Benjamin Lloyd-Hughes

I am wondering if it is possible to read.table repeatedly from a list of file names into a new list of table names. For example: filenames <- list.files() then with a function like rf <- function(i) { word??(filename[i]) <- read.table(filenames[i]) } I can't seem to find a function like word?? that will be the object of another operation. If this worked, then I could repeat

I collected eggs laid by Springtails everyday over 28 days after swich to isotopically enriched diet. The eggs were pooled at day 7, 14, and 28 (+ day 0 = initial value) and analyzed for isotopes. After the diet switch the isotopic values of the adults and eggs change towards those of the new diet. Here are the d13C values (y) of the eggs: x y 0 -22.2 0 -22.2 0 -22.2 0 -22.0 7