[BioC] DEseq version and R version compatibility

Thomas Girke thomas.girke at ucr.edu
Thu Oct 4 16:41:35 CEST 2012

There is no good reason not to keep R and Bioc fully up-to-date on a
Linux server for all users while maintaining older versions too. If they
have certain dependencies then one can easily configure things that
users can call a specific R version by its version number, e.g. calling
the latest version by typing R-2.15.2 instead of just R. A more generic
solution to this is usually to use a module system that administers
versions of any software not just R: http://modules.sourceforge.net/.
This can be extremely useful in the NGS analysis world since you will
end up installing new versions of all kinds of software (e.g. aligners,
assemblers, Perl/Python modules) almost every day. 


On Thu, Oct 04, 2012 at 12:24:46PM +0000, José Luis Lavín 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?
> 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
> 	[[alternative HTML version deleted]]

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