[BioC] DEseq version and R version compatibility

Sean Davis sdavis2 at mail.nih.gov
Thu Oct 4 14:42:51 CEST 2012

On Thu, Oct 4, 2012 at 8:24 AM, José Luis Lavín <jluis.lavin at 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R-2.13 is pretty outdated at this point.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.


> 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
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