similar to: Re: [BioC] 64-bit CPUs and bioconductor

[BioC] ANN: Introductory R and Bioconductor Mini Course , Seattle, April 12-14 We will present a short course on using Bioconductor, primarily aimed at analyzing microarray data, over 2 1/2 days in April. The course will be a mix of lectures and practical labs. Instructors: Robert Gentleman, Seth Falcon, Martin Morgan, and Nolwenn Le Meur Topics: Introduction to R Preprocessing of

Hi Patrick, Greetings from !(sunny) Pittsburgh. What's the scoop on RCurl on windows (XP)? I've tried to install RCurl_0.92-0.zip and RCurl_0.9-3.zip, with both R 2.7.2 and R 2.8.0 from the RGUI (utils:::menuInstallLocal), and get the error "Windows binary packages in zipfiles are not supported". which (according to google's one and only hit) comes from a perl script.

Hi again, I have been playing around with the order of loading packages, and as far as I can tell, there's nothing specific with affycoretools that's causing my Rgui to crash (i.e., shuts down and the Microsoft 'please send error report' box pops up). Instead, it has something to do with the order & type of packages that are loaded that add items to the menu bar by

mogene10stprobeset.db is generated with AnnotationDbi for mouse gene array. I don't find a package that seems generated by AnnotationDbi for exon arrays on the webpage you mentioned. Is it correct? On Tue, Oct 27, 2009 at 7:00 PM, Marc Carlson <mcarlson at fhcrc.org> wrote: > Hi Peng, > > I am not completely clear from your post what you want. ?But most of our > annotation

Hi Christian, Chuck (and lists) It seems that the problem may be the strange behaviour of 'unstack' inside a function. See this thread in the R mailing list: http://tolstoy.newcastle.edu.au/R/help/04/03/1160.html Anyway, I got round the problem by using 'aggregate' instead of converting to a list and then tapply to sum values of metric. Probably more efficient as well. Thanks

I think that you misunderstood 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

The warnings from make.packages.html() on the Apple Mac OS X platform can be dealt with as follows: ------------------------------------------------ (1) make.packages.html() uses the function tempdir() and attempts to create a temporary directory in the default location /tmp/ which fails due to the /tmp directory architecture on the Mac. I set up a .Renviron file in my user account

I currently set the Bioconductor repository in my .Rprofile using this code (which needs editing for every version number change of Bioconductor): # Choose repositories repos <- structure(c(CRAN="http://streaming.stat.iastate.edu/CRAN", CRANextra="http://www.stats.ox.ac.uk/pub/RWin",

I posted the following a little earlier on the quantian-announce list -- but it may be of interest here as well as this version contains all (but three, see below) packages from CRAN, and all of BioConductor. Quantian strives to provide the easiest way to set up a very complete scientific computing environment with a wide variety of tools -- including R, ESS, Ggobi, almost all of CRAN, all of

I posted the following a little earlier on the quantian-announce list -- but it may be of interest here as well as this version contains all (but three, see below) packages from CRAN, and all of BioConductor. Quantian strives to provide the easiest way to set up a very complete scientific computing environment with a wide variety of tools -- including R, ESS, Ggobi, almost all of CRAN, all of

Steffen, When the new biomaRt tries to load it errors out because I do not have RMySQL installed. There is not a Windows binary for RMySQL and it does contain C code that I do not know how to build. I do not use the MySQL option in biomaRt. Does RMySQL need to be a required dependency? Below is my screen output and sessionINfo. require(biomaRt) Loading required package: biomaRt Loading required

promptClass fails to identify methods associated with the class. Here is a fix: Index: promptClass.R =================================================================== --- promptClass.R (revision 41719) +++ promptClass.R (working copy) @@ -165,7 +165,7 @@ if (nmeths > 0) { .meths.body <- " \\describe{" for (i in 1:nmeths) { - .sigmat

"Gerard Tromp" <gerard.tromp at sanger.med.wayne.edu> writes: > Greetings, > > this is a follow-up to the mailing below. Seth Falcon replied and indicated > that he and several others were unable to replicate the problem. > Specifically he requested: > > ============ > We are not able to reproduce this issue. If you reinstall the > annotation packages

Dear R Developers, I am developing a package to submit to bioconductor. Right now, a gene-set sample data is saved as a data frame. Each row contains a probe set and its corresponding gene-set name ( mutiple probe -set may map to a gene-set name) . Is this type of data format OK to be submitted to bioconductor? Or I have to make it GeneCollectionSet class? ( If so, I have to change a lot of my

Mark, there is a fdr website link via Yoav Benjamini's homepage which is: http://www.math.tau.ac.il/%7Eroee/index.htm On it you can download an S-Plus function (under the downloads link) which calculates the false discovery rate threshold alpha level using stepup, stepdown, dependence methods etc. Some changes are required to the plotting code when porting it to R. I removed the

On 03/27/2014 02:13 AM, Ulrich Bodenhofer wrote: > I fully agree, Michael, that this would be a great thing to have! I have > often wondered why R and the standard packages are still sticking so > much to the old-style S3 flavor though S4 is part of standard R. I > acknowledge that backward compatibility is important, but, as far as I > got it, redefining a function or S3 generic as

Hello, I am attempting to install Bioconductor on 64 bit R. The installation of some bioconductor packages fails with the errors below. I would be very grateful for any help on how to resolve the issue. Best regards, Octavio Espinosa --------------------- Most of the bioconductor packages won't install, for examples 'Biobase' errors with: ** building package indices ...

Hello useRs, I'm trying to install bioconductor on ubuntu edgy eft and R 2.4.0. I have some error messages during installation, in particular for the package "affy" : "Error: package 'affy' required by 'makecdfenv' could not be found" I have tryed to install 'makecdfenv' with the command : getBioC("makecdfenv") But I have this message

Dear developers, has anyone experienced the problem described below? Is it a bug in handling interrupts in R? Best, Oleg -------- Original Message -------- Subject: Re: [BioC] 'recursive default argument' error in GOENTREZID2GO From: Diego Diez <diez at kuicr.kyoto-u.ac.jp> ...steps that use to reach me to that point. It happens with any environment, or at least annotation

Dear All, Thank you kindly for such detailed replies. I was looking to overlay data using algorithms so that i am able to tell which genes are differentially expressed due to changes in copy number. I did a pubmed search and found only 7 literature pieces all of which use in-house algorithms. I am yet to explore Gviz since it wouldn't work on R 2.14, would try it after upgrading to R 2.15.