similar to: Affymetrix Cancer Dataset

I don't know if this is the correct forum to ask the following question; however, when I search the aroma.affymetrix discussion group, it suggested that I should posted the question to r-help. Here it goes. I followed the instructions on aroma.affymetrix trying to install the packages; following are the steps: > install.packages(c("R.oo", "R.utils"),

Hello, I've got a DESCRIPTION file with a the first line: Package: Repitools But, when I run R CMD INSTALL Repitools I get: * installing *source* package Repitools ... ** R ** data ** inst ** preparing package for lazy loading Warning in FUN(X[[1L]], ...) : Created a package name, "2011-04-20 09:05:40", when none found ** help *** installing help indices ** building package

During installation of a package, Makevars/Makefile in src/ is processed. I've always considered the purpose of this for compiling native code. Is that it's solely purpose, or is it alright to use it also for non-code compilation purposes, e.g. building inst/ subdirectories on the fly? If not, are there other means to create non-static inst/ subdirectories during installation? The

Hi, I got an interesting programming challenge: How do you inspect an object which is assigned via delayedAssign() and that throws an error as soon as it is "touched" (=the value is evaluated)? Is it possible? MINIMAL EXAMPLE: $ R --vanilla > delayedAssign("foo", stop("Hey!")) (If you find this minimal example silly/obvious, please skip down to the real

Hello, I've been attempting to make a generic method that dispatches on the first argument, which can be either an S3 or an S4 class. This is as far as I've gotten. Any suggestions about what to try next ? library(aroma.affymetrix) library(GenomicRanges) setGeneric("analyse", function(x, y, ...) standardGeneric("analyse")) setMethodS3("analyse",

Hi List, I'm trying to install aroma.affymetrix, which depend on many packages, affyio is one of them. The task is done on 32-bit Linux without problem. The same task was done on Solaris 9 with R-2.5.1 without problem. Following is the error message when installation affyio. I did try to put a file stdint.h I got from the web in the path, but got more error messages. Jun root@biostatsun1

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Hi, sessionInfo() has been proven really useful, but you still often have to ask for additional information in order to help troubleshooting. For instance, for troubleshooting the aroma.affymetrix, it is very helpful to know what the current working directory is, for other packages certain system environment variables might be useful and so on. One solution could be to provide support for hook

Hi, I'm trying to remove/delete a directory usingR. I've tried the following with no success: % Rterm --vanilla > getwd() [1] "C:/Documents and Settings/hb/braju.com.R/aroma.affymetrix/test" > dir.create("foo") > file.info("foo") size isdir mode mtime ctime atime foo 0 TRUE 777 2007-02-28 14:52:10

Hello, I wonder if it is unwise to name a bundle the same as one of its packages. For instance, I now have a huge package called 'aroma' that I basically want to split up in several smaller packages, say 'aroma.core', 'aroma.io', 'aroma.explore', 'aroma.trial', 'aroma.deprecated' etc, which simplifies maintenance but also the overview. For

There are different way to make R classes. I know R.oo and S4. I'm wondering which one is the current popular one. Which one is current recommended when make new R packages? Thank you!

FYI, I'm sure the following is a temporary issue, but in case it slips through, I want to raise it here. On Windows 7 64-bit, running Rcmd check on R devel gives: * using R version 2.13.0 Under development (unstable) (2011-02-11 r54330) * using platform: x86_64-pc-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'aroma.core/DESCRIPTION' ... OK * this is

Dear all, we have an exciting PhD position applying HPC to the analysis of large scale cancer datasets. The post will suit an applicant from a strong computational background who wishes to apply their knowledge to help develop a better understanding of the processes that control how tumours develop. Details below:- High Performance Computing applied to cancer research: Computational analysis of

Hi! I would like to select probes (affy expression set) of genes that are "cancer-related". Conventionally the decision whether a gene is cancer-related or not is made by looking up the literature. Since this is not possible for all genes on the array I wonder if there is a way of doing this automatically? Best wishes Kristian -- _____ Dr Kristian Unger Imperial College London

Hi. Is it possible to make gpr from raw? library(aroma) #read gpr file gpr <- GenePixData$read("gpr123.gpr", path=aroma$dataPath) # gpr -> raw raw <- as.RawData(gpr) # raw -> ma ma <- getSignal(raw, bgSubtract=FALSE) ma.norm <- clone(ma) #normalization normalizeWithinSlide(ma.norm, "s") #ma -> raw raw2 <- as.RawData(ma) I want to make gpr data from

Hi everyone, My purpose is to read a .CEL file into R. The .CEL file was created from a .CAB by using DTT software found on Affymetrix website I read the .CEL file in R using ReadAffy as follows: > d2=ReadAffy(widget=T) and I complete the fields as required. It does not complain. For example I could find the description: > description(d2) Experimenter name: BB Laboratory: FFL Contact

Hi, I am trying to read in my Affymetrix CEL files (48 files, total ~600 MB) but I keep getting memory errors. Can somebody please help me with this. Or is therea remote server I can send my data to for computation? Any help is much appreciated. Thanks Dr. Tristan Coram Postdoctoral Research Associate Research Plant Pathologist/Geneticist United States Department of

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Dear fellow R-help members, I hope to seek your advice on how to parse/manage a dataset with hundreds of columns. Two examples of these columns, 'cancer.problems', and 'neuro.problems' are depicted below. Essentially, I need to parse this into a useful dataset, and unfortunately, I am not familiar with perl or any such language. data <- data.frame(id=c(1:10))

Hi, I have found an unwanted feature in the Rd to LaTeX convertion regarding \preformatted inside a \section. I have created an Rd example below, which generates an error in the following 'R CMD check' step * creating aroma.affine-manual.tex ... OK * checking aroma.affine-manual.tex ... ERROR LaTeX errors when creating DVI version. This typically indicates Rd problems. I believe