[Bioc-devel] maPlot Fold Change

Hello, In the documentation of maPlot, it doesn't state that the fold change is calculated as y / x. It would be good to have it stated, since x / y is just as valid. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___

Re: [Bioc-devel] deprecation of keepSeqlevels and renameSeqlevels

It's clear we're not going to agree. I will volunteer to maintain these, OK? I will maintain them anyway for my own use. Michael On Tue, May 21, 2013 at 2:34 PM, Hervé Pagès wrote: > > > On 05/21/2013 08:00 AM, Michael Lawrence wrote: > >> >> >> >> On Mon, May 20, 2013 at 10:36 PM, Hervé Pagès

Re: [Bioc-devel] deprecation of keepSeqlevels and renameSeqlevels

On 05/21/2013 02:34 PM, Hervé Pagès wrote: On 05/21/2013 08:00 AM, Michael Lawrence wrote: [...] So it looks like seqlevels<- is pretty powerful. Now I see that if I scroll down to the examples in the man page, I find the actual documentation. It's cool to learn that we can replace seqlevels

Re: [Bioc-devel] deprecation of keepSeqlevels and renameSeqlevels

On 05/21/2013 08:00 AM, Michael Lawrence wrote: On Mon, May 20, 2013 at 10:36 PM, Hervé Pagès mailto:hpa...@fhcrc.org>> wrote: Michael, On 05/20/2013 08:44 PM, Michael Lawrence wrote: On Mon, May 20, 2013 at 4:13 PM, Hervé Pagès mailto:hpa...@fhcrc.org>

Re: [Bioc-devel] R version in Bioc packages (was Re: [BioC] Package \'jmosaics\' not found)

On Tue, May 21, 2013 at 1:01 PM, Dan Tenenbaum wrote: > Hi Steffen, > > > > On Tue, May 21, 2013 at 12:40 PM, Steffen Neumann > wrote: >> Hi, >> >> On Tue, 2013-05-21 at 11:47 -0400, James W. MacDonald wrote: >>> Not that I can recall. But I do agree that it is at minimum redundant >>> and proba

Re: [Bioc-devel] R version in Bioc packages (was Re: [BioC] Package \'jmosaics\' not found)

Hi Steffen, On Tue, May 21, 2013 at 12:40 PM, Steffen Neumann wrote: > Hi, > > On Tue, 2013-05-21 at 11:47 -0400, James W. MacDonald wrote: >> Not that I can recall. But I do agree that it is at minimum redundant >> and probably just wrong to have R-version requirements for BioC packages. > > I

Re: [Bioc-devel] R version in Bioc packages (was Re: [BioC] Package \'jmosaics\' not found)

Hi, On Tue, 2013-05-21 at 11:47 -0400, James W. MacDonald wrote: > Not that I can recall. But I do agree that it is at minimum redundant > and probably just wrong to have R-version requirements for BioC packages. I'd like to disagree. BioC *promises* that stuff works together at a certain point

Re: [Bioc-devel] \VignetteIndexEntry

Hi Wolfgang, On Mon, May 20, 2013 at 2:00 PM, Wolfgang Huber wrote: > I am puzzled by the interpretation of the %\VignetteIndexEntry directive by > the build system. On > http://www.bioconductor.org/packages/devel/bioc/html/genefilter.html of the > four vignettes for this package, two are list

Re: [Bioc-devel] R version in Bioc packages (was Re: [BioC] Package \'jmosaics\' not found)

Not that I can recall. But I do agree that it is at minimum redundant and probably just wrong to have R-version requirements for BioC packages. And seriously? 500 packages? I find that surprising. Best, Jim On 5/21/2013 11:38 AM, Martin Morgan wrote: Pulling this over to Bioc-devel. It's temp

[Bioc-devel] R version in Bioc packages (was Re: [BioC] Package \'jmosaics\' not found)

Pulling this over to Bioc-devel. It's tempting to strip this from the DESCRIPTION files of the ~500 packages that include it. It's not useful in the context of the Bioconductor release schedule, and makes a forward promise that cannot be guaranteed. Is this something that has come up before?

Re: [Bioc-devel] deprecation of keepSeqlevels and renameSeqlevels

On Mon, May 20, 2013 at 10:36 PM, Hervé Pagès wrote: > Michael, > > > On 05/20/2013 08:44 PM, Michael Lawrence wrote: > >> >> >> >> On Mon, May 20, 2013 at 4:13 PM, Hervé Pagès > > wrote: >> >> Hi, >> >> >> On 05/20/2013 03:15 PM, Michael Lawrence wrote: >> >>