Re: [Bioc-devel] VariantAnnotation: writeVcf fails for factors with unused levels

2014-02-07 Thread Michael Lawrence
On Fri, Feb 7, 2014 at 12:09 AM, Julian Gehring wrote: > Hi, > > I got two more (with VariantAnnotation_1.9.35, Rsamtools_1.15.27). They > may be related to what we discussed before, so I'm leaving them in this > thread. > > ** Some example data > > #+BEGIN_SRC R > library(VariantAnnotation) >

[Bioc-devel] Fwd: Bioconductor git-svn bridge is available

2014-02-07 Thread Dan Tenenbaum
Forgot to copy the list - Forwarded Message - From: "Dan Tenenbaum" To: "Mike" Sent: Wednesday, February 5, 2014 2:12:18 PM Subject: Re: [Bioc-devel] Bioconductor git-svn bridge is available See http://www.bioconductor.org/developers/how-to/git-svn/#bridge-to-release-version Bas

[Bioc-devel] New package: biosvd

2014-02-07 Thread Anneleen Daemen
Everyone, *biosvd* is a new package available in BioC 2.14 devel. Interested in a global picture of the dynamics in your data set in terms of patterns of similar regulation and function or similar cellular state and biological phenotype? Regardless of the nature of your data set (expression, pro

Re: [Bioc-devel] svn repository for data experiment packages now having branches too

2014-02-07 Thread Bernd Fischer
Dear Herve! Please start using the same x.y.z versioning scheme as for software packages with the new release for data experiment packages, with even y for release and odd y for devel. I just copied code from devel to the release version of my package and asked myself which version number to u

Re: [Bioc-devel] VariantAnnotation: writeVcf fails for factors with unused levels

2014-02-07 Thread Julian Gehring
Hi, I got two more (with VariantAnnotation_1.9.35, Rsamtools_1.15.27). They may be related to what we discussed before, so I'm leaving them in this thread. ** Some example data #+BEGIN_SRC R library(VariantAnnotation) example(VRanges) ## gives us 'vr' and 'vcf' vr_small = vr width