Hello Sean,

The main problem with updating the R version of the servers is that I'm not
the SysAdmin, and he told me that they couldn't update it at the moment
because they have some processes and pipelines that need the old R version
(2.13), so he can't update it (weird, isn't it?). That's why I was looking
for such strange compatibility...
Anyway, due to my current low level on R scripting, when I come across a
command that isn't functional I don't really know what to do but trying to
use another manual version hoping the code there will fix it...but I've had
no luck with that at the moment. That's why I asked about this.
I'll keep trying to make DEseq work, but I begin to feel stupid, reading
everybody seems to be able to run it except myself.

Thank you for your swift answer, anyway

Best wishes

JL

2012/10/4 Sean Davis <sdavis2@mail.nih.gov>

> On Thu, Oct 4, 2012 at 8:24 AM, José Luis Lavín <jluis.lavin@unavarra.es>
> wrote:
> > Dear all,
> >
> > First of all I'd like to apologize for bothering you with such a naive
> > question, but I've been told that this is the place to ask about this
> > particular issue.
> >
> > I'm trying to perform a Differential Expresion analysis on some RNA-seq
> > experiments using DEseq package. I'm not very fluent with R yet, and I'm
> > facing some problems while using DEseq for the analysis. In my
> institution
> > the R version of the Linux servers system is 2.13.0 and the version I
> > installed in my windows terminal is 2.15.2.
> > I've retrieved multiple DEseq manual versions from the internet (dated
> > 19/01/2010, 21/04/2011 and 12/04/2012) , but some R commands vary from
> one
> > to another and some are not supported in one or the other R versions I
> have
> > available. I need the R script to work in both versions and I don't
> really
> > know how to achieve it...
> > Could you please help me solving this giving me some kind of advice on
> how
> > to get a functional and compatible script to be used with both R
> versions I
> > previously stated?
>
> Hi, José.
>
> The versions of DEseq are matched to the versions of bioconductor
> which are matched to the versions of R.  In other words, the only way
> to match the versions of DEseq between two machines is to use the same
> version of R on both.  Installing R in your home directory is not
> difficult, so I'd suggest you try that on your linux cluster since
> R-2.13 is pretty outdated at this point.
>
> Also, you'll want to ALWAYS use biocLite() to install packages, as
> detailed on the bioconductor website.  This can avoid headaches with
> version mismatches in the future.
>
> Sean
>
>
> > Thanks in advance for your kind support.
> >
> > With best wishes
> >
> > JL
> >
> > --
> > --
> > Dr. José Luis Lavín Trueba
> >
> > Dpto. de Producción Agraria
> > Grupo de Genética y Microbiología
> > Universidad Pública de Navarra
> > 31006 Pamplona
> > Navarra
> > SPAIN
> >
> >         [[alternative HTML version deleted]]
> >
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
-- 
Dr. José Luis Lavín Trueba

Dpto. de Producción Agraria
Grupo de Genética y Microbiología
Universidad Pública de Navarra
31006 Pamplona
Navarra
SPAIN

	[[alternative HTML version deleted]]

