search for: aroma

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 convenience, one could have a wrapper package ...

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"), contriburl="htt...

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....

...ia.1252 LC_CTYPE=English_Australia.1252 [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C [5] LC_TIME=English_Australia.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.4.4 Biobase_2.8.0 aroma.affymetrix_1.7.0 [4] aroma.apd_0.1.7 affxparser_1.20.0 R.huge_0.2.0 [7] aroma.core_1.7.0 aroma.light_1.16.0 matrixStats_0.2.1 [10] R.rsp_0.3.6 R.cache_0.3.0 R.filesets_0.8.3 [13] digest_0.4.2 R.utils_1.4.4 R.oo_1.7.3 [16] R.methodsS3_...

.../ subdirectories during installation? The immediate need I have right now is that untar an archive to inst/testScripts/. The reason why I need this is that a package can only contain pathnames of length <= 100 characters (restriction in the tar file format), and mine are longer than that, e.g. aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20080730,100K,BPN,alleleSpecific.R [115 chars]. See also http://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora/aroma.affymetrix-00check.html . One strategy is to create a local tar file referring to files syste...

...sue, 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 package 'aroma.core' version '1.9.4' * checking package dependencies ... OK * checking if this is a source package ... OK * checking for executable files ... OK * checking whether package 'aroma.core' can be installed ... OK * checking...

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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 p...

...ed assignment? Is it possible to test if this is a delayed assigned or not? BACKGROUND: The background to this is where I have a function in the R.oo package that scans namespaces for functions with a certain class attribute. For this I use is.function() and inherits() to inspect each object. An aroma.affymetrix user reported on a problem that boiled down to the following: # source("http://bioconductor.org/biocLite.R"); biocLite("hgu133a.db") > library("hgu133a.db") > is.function(hgu133aPFAM) Error: hgu133aPFAM is defunct. Please use select() if you need acce...

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 the Rd code itself explains the details, the reasons, and the work around. Should it be reported as a bug? Best wishes Henrik Bengtsson...

I'm rather frustrated in trying to run the examples on the robustSmoothSpline. No matter what packages I load, I still come up with the error as follows. Error: could not find function "robustSmoothSpline" Am I missing something?

Hi, in my package, I've got a 'configure' file in the root, e.g. aroma.affymetrix/configure. (I've also got a configure.win, which works just fine on Windows). This file must be executable (has a proper file mode) for 'R CMD INSTALL'/install.packages() to work, otherwise one gets: * installing *source* package 'aroma.affymetrix' ... ERROR: 'co...

...en McKinney [smckinney at bccrc.ca] Sent: Thursday, November 19, 2009 2:21 PM To: Kevin R. Coombes; r-devel at r-project.org Subject: Re: [Rd] R Usage Statistics Hi Kevin, What a surprising comment from a reviewer for BMC Bioinformatics. I just did a PubMed search for "limma" and "aroma.affymetrix", just two methods for which I use R software regularly. "limma" yields 28 hits, several of which are published in BMC Bioinformatics. Bengtsson's aroma.affymetrix paper "Estimation and assessment of raw copy numbers at the single locus level." is already ci...

Hello, I've been having some trouble working with the aroma package and have realized that it's my ebimage is at the root of the problem. The package builds but during testing it fails because of an undefined symbol as seen below: installing to /usr/local/lib64/R/library/EBImage/libs ** R ** inst ** preparing package for lazy loading ** help **...

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

...ut files are in the following order: > > oligo.prest.out for parse.RData to work. Produces the next input file > > oligolista for Korrelation.RData to work, which also needs the input file > > 8_SkBr _13433630.gpr. > > > The function GenePixData can be found in the aroma package. > > Thank you for your help, 1. Package kth is unavailable for us. 2. I do not know anything about a package called "aroma", it is neither on CRAN nor in the BioC repositories. 3. Can you please also try to make your example smaller? 4. The convention is to save R ob...

waited for the aroma of burnt electronics. There wasn't any so I went to the next room and plugged in a telephone on the wall outlet. I picked up the handset and it rang my asterisk box. I dont have any phone service. The phone is working fine and have used it for hours listening to podcasts. And I can plug...

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 functions of sessionInfo(), which package then can register and append to the 'sess...

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", "AffymetrixCelSet", function(x, y, z, ...) { x; UseMethod("analyse") } ) setGeneric("analyse") setMethod(...

...test if this is a delayed assigned or not? > > > BACKGROUND: > The background to this is where I have a function in the R.oo package > that scans namespaces for functions with a certain class attribute. > For this I use is.function() and inherits() to inspect each object. > An aroma.affymetrix user reported on a problem that boiled down to the > following: > > # source("http://bioconductor.org/biocLite.R"); biocLite("hgu133a.db") >> library("hgu133a.db") >> is.function(hgu133aPFAM) > Error: hgu133aPFAM is defunct. Please us...