similar to: read.table without sep

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 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 have the attached data called "new" as data.frame. First I have only three columns called Var1, Var2 and Freq and with bind I attached the column test for a color specification (TEST DATA below). With this plot function (require packages lattice) dotplot(reorder(Var1, rep(score, cl.count)) ~ Freq | Var2, data = DATA, origin = 0, type = c("p",

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 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

Hi everybody, I have a problem when trying to do the quality control with the packages simpleaffy and affyQCReport with the drosophila chip 2.0 At first I got the messeage, that the *.qcdef file is not there. I followed the instructions in tha manual and created the file like that: array drosophila2cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD

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

Thanks a lot, James!! The problem is fixed. On the version 1.4.0 Mac/darwin (the latest available version for this system) the function read.table (which is called from read.delim etc., too) has the bug you explained. Inserting the row nlines <- nlines+1 after lines <- c(lines, line) removes this bug. M. On Friday, February 22, 2002, at 02:33 PM, james.holtman at convergys.com

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 trying to create a .jpg file with multiple graphs on it. I am creating this file through a java servlet which connects to R using RServe. In the code below, col is an int array which has a list of the col numbers of the data file whose data i have to use for plotting. c=new Rconnection();

Hello, I'm using recursive SVM script (rSVM - http://www.stanford.edu/group/wonglab/RSVMpage/R-SVM.html ) on some microarray data. The data to be input are log2, as numeric matrix w/ attributes -- str(svm_num_mat) num [1:10, 1:12340] 13.1 13.1 13.1 13.1 13.0 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:10] "rma_log2_con_sample_1"

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

Hi, Reading help("Documentation"), I'm led to believe that a help call like: ?myFun(x, sqrt(wt)) Will search for help on the appropriate method in the case that myFun is generic. This isn't working for me. Here is an example using the Biobase package: ## If Biobase is not installed source("http://bioconductor.org/biocLite.R") biocLite("Biobase")

On 10/11/2006 2:48 PM, Seth Falcon wrote: > Hi, > > Reading help("Documentation"), I'm led to believe that a help call > like: > > ?myFun(x, sqrt(wt)) > > Will search for help on the appropriate method in the case that myFun > is generic. This isn't working for me. Here is an example using the > Biobase package: > > ## If Biobase is

Dear all, Is there a way with Bioconductor in which I can convert such EnSemBL probe names into the standard gene names? AFFX-M27830_5_at AFFX-M27830_M_at ENSG00000000003_at ENSG00000000005_at ENSG00000000419_at - Gundala Viswanath Jakarta - Indonesia

Dear R-helpers & bioconductor Sorry for cross-posting, this concerns R-programming stuff applied on Bioconductor context. Also sorry for this long message, I try to be complete in my request. I am trying to write a subset method for a specific class (ExpressionSet from Bioconductor) allowing selection more flexible than "[" method . The schema I am thinking for is the following:

The following code results in a seg fault. > sessionInfo() R version 2.6.0 Under development (unstable) (2007-06-21 r42013) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] stats graphics