search for: bcarvalh

...y configured and compiled it, which means I'm able to run it from the R-2.4.0/bin directory. I want to do a system wide installation (via 'sudo make install') and help2man fails, ie, when I execute the installation command mentioned previously I get: make[1]: Entering directory `/home/bcarvalh/R-2.4.0/m4' make[1]: Nothing to be done for `install'. make[1]: Leaving directory `/home/bcarvalh/R-2.4.0/m4' make[1]: Entering directory `/home/bcarvalh/R-2.4.0/tools' make[1]: Nothing to be done for `install'. make[1]: Leaving directory `/home/bcarvalh/R-2.4.0/tools' make[...

...igured and compiled it, which means I'm able to run it from the R-2.4.0/bin directory. I want to do a system wide installation (via 'sudo make install') and help2man fails, ie, when I execute the installation command mentioned previously I get: make[1]: Entering directory `/home/bcarvalh/R-2.4.0/m4' make[1]: Nothing to be done for `install'. make[1]: Leaving directory `/home/bcarvalh/R-2.4.0/m4' make[1]: Entering directory `/home/bcarvalh/R-2.4.0/tools' make[1]: Nothing to be done for `install'. make[1]: Leaving directory `/home/bcarvalh/R-2.4.0/tools' make[...

...t;- foo(arg1) so, inside foo() I'd like to be able to get the string "x". if, foo(arg1) was used insted, I'd like to get NA. thank you very much, b -- Benilton Carvalho PhD Candidate Department of Biostatistics Bloomberg School of Public Health Johns Hopkins University bcarvalh at jhsph.edu

...derstood me. As far as I know, RMA does three things: background correction, quantile normalization, and summary from probes to probesets. I want the probe values after background correction and quantile normalization but before the summary. On Sat, Dec 26, 2009 at 12:07 PM, Benilton Carvalho <bcarvalh at jhsph.edu> wrote: > pm(data) > > b > > On Dec 26, 2009, at 2:21 PM, Peng Yu wrote: > >> I use the following code to do RMA. I'm wondering how get the probe >> level values before the summary to the probeset level values. >> >> library(oligo) >&...

Hi Everyone, I want to generate some random numbers according to some empirical distribution. Therefore I am looking for the inverse of an empirical cumulative distribution function. I haven't found any in R. Can anyone give a pointer? Thanks, Geoffrey _______________________________________________________=0A= =0A= =0A= The information in this email or in any file attached

Hi everyone, it's been a while I've been trying to save a plot created via lattice:::xyplot if I have a file tst.R with the following code: y <- rnorm(100) x <- rnorm(100) z <- sample(letters[1:4], 100, rep=T) library(lattice) bitmap("tst.png") xyplot(y~x|z) dev.off() and I source it, I get the tst.png file, which is a blank page. If I copy and paste instead, I

I am running a very long loop and would like to save intermediate results in case of a system or program crash. Here is the skeleton of what my code would be: for (i in 1:zillion) { results[[i]]<-do.something.function() if (logical.test(i)) {save(results, "results.tmp")} } logical.test would test to see if i/1000 has no remainder. What R function would test that?

Hi everyone, sorry if this was discussed before (and in this situation, could you please point me to the discussion in the archive? My search didn't seem to be effective). Is there a way of getting the names of objects in a .rda file without having to load it? Thank you very much, benilton -- PhD Candidate Department of Biostatistics Bloomberg School of Public Health Johns Hopkins

Hi all: A short question: For example, a=[3,4,6,2,3], obviously the 3rd entry of the array has the maxium value, what I want is index of the maxium value: 3. is there a neat expression to get this index? Thank you! Best, Feng [[alternative HTML version deleted]]

I want to remove the column names from a data frame. I do it the long way, can any body show me a better way ? df= data.frame(chrN= c(“chr1”, “chr2”, “chr3”), start= c(1, 2, 3), end= c(4, 5, 6), score= c(7, 8, 9)) df #I write a txt file without row or column names write.table(df,"df1.txt",sep='\t',quote=FALSE,row.names=F,col.names=F) #then I read it with the header = F

Dear R users, I used R to draw many histograms and I would like to automatically save them into a jpeg file. I tried the following code since I know .ps file could be saved like this way: postscript("AYA_ELA.jpeg",horizontal=F,onefile=T) ......#some funtions inside here dev.off() There was a jpeg file, however, there is no pictures inside. Any suggestion? Thanks. Rebecca

Hi everyone, I have 2 environments (2 different R sessions) as described below: Session 1: Name of the environment: "CrlmmInfo" Objects in the environment: index1: logical index - length 238304 index2: logical index - length 238304 priors: list of 4 - (matrix 6x6, 2 vectors of length 6, vector of length 2) - all num params: list of 4: centers [238304 x 3 x

Hi everyone, I have 2 environments (2 different R sessions) as described below: Session 1: Name of the environment: "CrlmmInfo" Objects in the environment: index1: logical index - length 238304 index2: logical index - length 238304 priors: list of 4 - (matrix 6x6, 2 vectors of length 6, vector of length 2) - all num params: list of 4: centers [238304 x 3 x

I read somewhere that t.test is equivalent to a hypothesis testing for one way ANOVA. But I'm wondering how they are equivalent. In the following code, the p-value by t.test() is not the same from the value in the last command. Could somebody let me know where I am wrong? > set.seed(0) > N1=10 > N2=10 > x=rnorm(N1) > y=rnorm(N2) > t.test(x,y) Welch Two Sample t-test data:

Hi all, I recently updated my to R 2.6.0 and tseries package ?tseries? version: 0.10-11. When i was using R Version 2.3.1 (2006-06-01) with tseries 'tseries' version: 0.10-7, the code > garch(dflnRCLC1) ***** ESTIMATION WITH ANALYTICAL GRADIENT ***** Call: garch(x = dflnRCLC1) Coefficient(s): a0 a1 b1 4.985e+00 1.880e-01 6.210e-14 > worked very

Hi Everyone, After searching the subject and not being successful, I was wondering if any you could explain me the idea behind the following fact: all(NULL == 2) ## TRUE any(NULL == 2) ## FALSE Thanks a lot, Benilton -- Benilton Carvalho PhD Candidate Department of Biostatistics Johns Hopkins University

Hi Everyone, I often use the 'safe prediction' feature available through glm(). Now, I'm at a situation where I must use biglm:::bigglm. ## begin example library(splines) library(biglm) ff <- log(Volume)~ns(log(Girth), df=5) fit.glm <- glm(ff, data=trees) fit.biglm <- bigglm(ff, data=trees) predict(fit.glm, newdata=data.frame(Girth=2:5)) ## -1.3161465 -0.2975659

Hi, First of all, I apologize for sending out this message, as I'm sure the answer is on the archives, but I just can't find it. Not long ago, there was a discussion about building Windows packages from the source code and someone posted a link to a website to which we could submit the source and get the Windows version a while later. Could someone point me to that website or to

Hi, Here's one toy example that shows what I believe to be a problem with plot.lm. This was brought up by another user (Marcos Tadeu Andrade Cordeiro). I took a look at the source and the problem appears to be related to the fact that you need to reorder the data by the group means and the correct order of the labels is lost. set.seed(2) a <- rnorm(50,0,2) x <- rep(seq(10, 50,

Hi Everyone, when building (say) R-2.4.0 from the source, is it still the recommendation to use GCC 3.4? Thank you very much, Benilton Carvalho PhD Candidate Department of Biostatistics Johns Hopkins University