[BioC] Package qvalue - can it be installed without TCL-TK support?

[Bernd Klaus]

Hi Guiseppe,

If I may shamelessly promote a package from my former group,

fdrtool (CRAN)

http://strimmerlab.org/software/fdrtool/

essentially uses the qvalue algorithm if you give it p-values,
so the results should be the same.

Best wishes,

Bernd


On Fri, 23 May 2014 09:05:15 -0700
Peter Langfelder <peter.langfelder at gmail.com> wrote:

> Another solution is to find an old version of qvalue, e.g., here:
> 
> http://cran.r-project.org/src/contrib/Archive/qvalue/
> 
> The version 1.1.1 is, to the best of my knowledge, the last that did
> not use the graphical interface and the Tcl/Tk that comes with it.
> 
> Peter
> 
> 
> On Fri, May 23, 2014 at 8:51 AM, Giuseppe Gallone
> <giuseppe.gallone at dpag.ox.ac.uk> wrote:
> > John
> >
> > thanks, I will try what you suggested.
> >
> > Best wishes
> > Giuseppe
> >
> >
> > On 05/23/14 15:31, John Blischak wrote:
> >>
> >> A short-term solution would be to download the source code and just
> >> directly use the qvalue function.
> >>
> >>   wget
> >>
> >> http://bioconductor.org/packages/release/bioc/src/contrib/qvalue_1.38.0.tar.gz
> >>   tar xzf qvalue_1.38.0.tar.gz
> >>
> >> Then source the code in R:
> >> source("qvalue/R/qvalue.R")
> >>
> >> If you wanted to install, you could edit the source code. I'd imagine
> >> deleting the function qvalue.gui and removing the references to tcltk in
> >> the package DESCRIPTION and NAMESPACE would allow you to install it from
> >> source.
> >>
> >> John
> >>
> >>
> >> On Fri, May 23, 2014 at 7:44 AM, Giuseppe Gallone
> >> <giuseppe.gallone at dpag.ox.ac.uk <mailto:giuseppe.gallone at dpag.ox.ac.uk>>
> >>
> >> wrote:
> >>
> >>     Hi
> >>
> >>     I need the qvalue package however I don't need the TCL-TK interface.
> >>
> >>     My R installation was compiled without native TCL-TK support and it
> >>     is inconvenient for me atm to reinstall/replace etc to add support.
> >>
> >>     As a consequence, as it stands it seems I cannot get qvalue to work
> >>     on my system.
> >>
> >>     Does anybody know of a way to install and run qvalue excluding the
> >>     TCL-TK bindings?
> >>
> >>     Best regards
> >>     Giuseppe
> >>
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> >>
> >
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