similar to: Need your help on R & BioC exploration

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

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

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.

[ I hope this is not considered off-topic for the list: A new Quantian release was just announced, and it contains even more R. As before, we have R (now 2.2.1), ESS, Ggobi, Rpy, several BioInfo tools -- but now we also have RSPerl, JGR, rJava and more. A full sync to CRAN and BioC as of Feb 25, 2006 now yields dim(installed.packages())[1] of 877. Feedback welcome, but

[ I hope this is not considered off-topic for the list: A new Quantian release was just announced, and it contains even more R. As before, we have R (now 2.2.1), ESS, Ggobi, Rpy, several BioInfo tools -- but now we also have RSPerl, JGR, rJava and more. A full sync to CRAN and BioC as of Feb 25, 2006 now yields dim(installed.packages())[1] of 877. Feedback welcome, but

(xposted to bioc-devel and r-devel as I feel it is relevant to both communities) As someone whose body of work is likely to consist mostly of infrastructural packages and research directly in computing I wholeheartedly agree with Kasper's suggestion that we as a community should work to provide and use package citations. I borrow heavily from existing work in terms of both concept and

[ Reposting this here as this Quantian release contains - all CRAN packages as of December 10, 2005 * except the Windows only ones (BRugs, mimR, rcom, RWinEdt) * and three that would not build (Rlsf, ROracle, rJava) for lack of Java, Oracle or rlsf - all BioC packages for release 1.8 * excecpt RMAGEML (needs Java) - for a total of over 800 R packages - a

[ Reposting this here as this Quantian release contains - all CRAN packages as of December 10, 2005 * except the Windows only ones (BRugs, mimR, rcom, RWinEdt) * and three that would not build (Rlsf, ROracle, rJava) for lack of Java, Oracle or rlsf - all BioC packages for release 1.8 * excecpt RMAGEML (needs Java) - for a total of over 800 R packages - a

I'm trying to load an annotation file on a new R installation on a new machine (Win 7 x64, R 2.15.0) Loading this package fails; I've tried re-installing R and BioC from scratch, including all new packages etc, to no avail. Any ideas? > require("hugene10sttranscriptcluster.db") Loading required package: hugene10sttranscriptcluster.db Loading required package: AnnotationDbi

[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

On Wed, Aug 13, 2008 at 6:56 AM, Laurent Gautier <lgautier@gmail.com> wrote: > There is a chance that further changes in the handling of plotting > devices event appear; > I think that there is an ongoing effort to bring new features for R-2.8. > > What about bumping that to r-devel ? (Sorry if you already did and I missed > it). > The solution you came up with could be

[CC:ing package maintainer of 'impute' package and crossposting to r-devel and bioc-devel because this affects both audiences] Hi, the 'impute' package is published both on CRAN and Bioconductor; http://cran.r-project.org/web/packages/impute/ http://bioconductor.org/packages/2.3/bioc/html/impute.html The one on CRAN is v1.0-5, and the one on BioC is v1.14.0. The two

Dear R user, I am a biochemist/bioinformatician, at the moment working on protein clusterings by conformation similarity. I only started seriously working with R about a couple of months ago. I have been able so far to read my way through tutorials and set-up my hierarchical clusterings. My problem is that I cannot find a way to obtain information on the rooting of specific nodes, i.e. of

[cross-posted to R-devel and bioc-devel] Hi, I am trying to implement a 'sort' method in one of the CRAN packages I am maintaining ('apcluster'). I started with using setMethod("sort", ...) in my package, which worked fine. Since many users of my package are from the bioinformatics field, I want to ensure that my package works smoothly with Bioconductor. The problem

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

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

Call for Workshops 8th IEEE International Conference on eScience October 8-12, 2012 Chicago, IL, USA The 8th IEEE eScience conference (e-Science 2012), sponsored by the IEEE Computer Society's Technical Committee for Scalable Computing (TCSC), will be held in Chicago Illinois from 8-12th October 2012. The eScience 2011 conference is designed to bring together

Call for Workshops 8th IEEE International Conference on eScience October 8-12, 2012 Chicago, IL, USA The 8th IEEE eScience conference (e-Science 2012), sponsored by the IEEE Computer Society's Technical Committee for Scalable Computing (TCSC), will be held in Chicago Illinois from 8-12th October 2012. The eScience 2011 conference is designed to bring together

Or maybe the "right" concept is that "numeric" is a virtual class with 3 subclasses: "complex", "double", and "integer". Anyway it's probably too late for implementing the "right" concept so it doesn't really matter. Thanks Martin for offering to fix the as(1L, "numeric") bug. Very much appreciated. I guess that means

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