similar to: Summary: read.table on Mac OS X, CARBON vs. DARWIN

Hi, I use write.table() to write a file to an external xls file. the column names left-shift one position in output file. I check with col.names() row.names(), the file is fine. How to prevent the shifting? I71 I111 I304 I307 I305 I306 I114 I72 AFFX-BioB-5_at 6.66435 6.787807 5.335962 5.250163 6.47423 5.882104 5.965109 6.591687195 AFFX-BioB-M_at 6.163227 5.965427 4.665569 2.743531 6.097244

Dear R user, I am trying to convert the contents of a date.frame to a matrix. Since there are negative values in the date.frame, when I use data.matrix(x, rownames.force = NA), the resulting matrix is not the same as the original one. Basically I think R treats the numbers in the date.frame as character and converts it to corresponding numerics. Any idea on this issue? Many Thanks, Hongyuan

I am very new to R. I was trying to load some publicly available Expression data in to R. I used the following commands mydata<-read.table("dataALLAMLtrain.txt", header=TRUE, sep ="\t",row.names=NULL) It reads data without any error Now if I use edit(mydata) It shows only 3916 entries, whereas the actual file contains 7129 entries) My data is something like Gene Description

Hello, I am looking for an explanation and/or fix for a discrepancy in the behaviour of the R lm.influence() function [ version R 1.5.0 (2002-04-29) ] and the same function in Splus [ Splus version 5.1 release 1, running on SGI IRIX 6.2]. The discrepancy is of concern because I am migrating some Splus scripts to R and need to ensure consistency of results. Specifically, when I fit a glm()

Hello all, I have a data file table.txt which i have attached. I am trying to pass the columns as arguments to a function "totnorm" where i am displaying a total normalization plot. The function is given below: totnorm<-function(x,y){scale<-sum(x)/sum(y);xlab<-colnames(x);ylab<-colnames(y);x1<-x[[1]];y1<-scale*y[[1]];plot(x1,y1,xlab=xlab,ylab=ylab,col=6, col.lab=4);}

Hello all, I have a data file table.txt which i have attached. I am trying to pass the columns as arguments to a function "totnorm" where i am displaying a total normalization plot. The function is given below: totnorm<-function(x,y){scale<-sum(x)/sum(y);xlab<-colnames(x);ylab<-colnames(y);x1<-x[[1]];y1<-scale*y[[1]];plot(x1,y1,xlab=xlab,ylab=ylab,col=6, col.lab=4);}

The 'read.table' function appears to be up to 10X slower in R 1.4.0 than R 1.3.1 for some of the data sets I read in. I was comparing the source code for the 2 versions and see that it was rewritten in R 1.4.0. I think I found out what part of the problem might be. I was comparing R1.3.1 and R1.4.0 code and it appears that a statement is missing in some of the code for R 1.4. This is

Hello, I am trying to do an ANOVA on a microarray data set consisting of 22690 elements. The ANOVA is fine, but when I try to put the data in a frame in order to exporting it, I get a stack overflow. I have found documentation on dynamic memory in R, but not on how to increase the stack size. The code I'm using is below. If anyone has any suggestions for a workaround here, I'd

Hello all, I am trying to perform ANOVA on my sample data given below to see if any gene(column 1 stands for gene names) is differentially expressed after subjecting it to the 6 different experiments(columns 2 to 7 are experiments). Gene 14A_U133A_Detection 14B_U133A_Signal 88A_U133A_Signal 88B_U133A_Signal 183A_U133A_Signal 183B_U133A_Signal AFFX-BioB-5_at 403 409.3 611.5

I have a data frame which has the following data. data<-read.table("table.txt",header=TRUE) data X14A_U133A_StatPairs X14A_U133A_Detection X14B_U133A_Signal 1 AFFX-BioB-5_at 403.0 409.3 2 AFFX-BioB-M_at 757.3 574.4 3 AFFX-BioB-3_at 284.4 327.3 4 AFFX-BioC-5_at

Dear all, i try to plot with ggplot2. Therefor I have an matrix with 3 colums. With cbind I add an additional column called "col". I need this column "col" because in a later step and want to specify here some plot details which I will get from another analysis If I want to plot with this code, I have the problem that the legend is wrong. Blue changed to green and green to

i was searching for the source of bca.ci, a function of the package boot. I tried require(boot, keep.source=TRUE) but again the source was not viewable. How should i do? Best regards Meinhard Ploner ---------------- PS > version _ platform i386-apple-darwin8.8.1 arch i386 os darwin8.8.1 system i386, darwin8.8.1 status major 2

Hello! Maybe "frame" is not the right term in this context. I explain my problem by example code: fun2 <- function(objName, add) { ## the object "objName" should be increased by "add", ## but the evaluation should be done in the calling function (here: fun1) ## ...... what's the right code?? } fun1 <- function() { x <- 1 fun2("x",

I am new on R, so I have a maybe naive question: if I have many large data.frames and I use only one or two per session, what's the best way? If all are stored in the actual .Rdata, the system gets slow. On the other hand, I wouldn't like to make a separate package for the data. Should I save it with save() and then remove it with rm() ? Could I reload it then? Thanks for suggestions

Hi R user! What is the fastest way to export a large matrix or vector to a MySQL database? The use of data.frame() and dbWriteTable() makes the process slow, so is there any <direct> alternative? Regards Meinhard Ploner

Hello! What is wrong on my system? I have downloaded today R 1.9.1 on my PC with Windows. plot.table isn't available in package <base> and neither in package <graphics> (as suggested after ?plot.table). Kind regards Meinhard Ploner [[alternative HTML version deleted]]

Hi! Since August I am using emacs on my Macintosh to edit the R objects. I have installed R 1.9.1, Mac OS X 10.3.5 and GNU Emacs 21.2.1. However there are some issues I haven't resolved: a) switch the caps lock key to the meta key (and when this is not possible, switch the alt/option key to the meta). The switch should work only within emacs! b) having different colors for the code,

Hi! I have R 1.9.1, Mac OS X 10.3.5, GNU Emacs 21.2.1 and ESS 5.2.3. I installed today the ESS by not changing ess-site.el, but creating .emacs in $home with the single line: $ cat ~/.emacs (load "/usr/local/lib/ess-5.2.3/lisp/ess-site") If I start now emacs and then R (with M-x R) then I get: > options(STERM='iESS', editor='emacsclient') but using fix() oder

It's possible to overlap an external image (jpg or pdf) with a plot generated with R? Specifying the image as the background of the plot might not be possible... any idea? thanks Meinhard Ploner

hi! I tried to build a very simple package with NAMESPACE file, such that datasets are loaded only dynamically. > a2 <- function(x=a1) x+4 > a1 <- 1:10 > package.skeleton("aaa", list=c("a1", "a2")) Then I modified the help files and added the file NAMESPACE with these 2 lines: useDynLib(aaa) export(a1, a2) Then "R CMD BUILD aaa" works