[BioC] DEseq version and R version compatibility

Simon Anders anders at embl.de
Thu Oct 4 15:40:23 CEST 2012

Hi Jose

On 2012-10-04 15:30, José Luis Lavín wrote:
> 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.

A rather fundamental issue is that bioinformatics is a rapidly 
developing subject, and you have to stay current. Working with software 
version older than a few months is usually asking for trouble, 
especially when you are using cutting-edge techniques such as 
high-throughput sequencing.

So: In the long run, there is simply no way getting your work done if 
you don't get a system with _current_ software. Either find a more 
helpful system administrator (yours is either lazy or incompetent: there 
is no problem in having two versions of R installed on the same 
machine), or learn to do that yourself.

And never assume that there is any point in using a software manual vor 
version X of some software if what you have installed is version Y. Why 
should this ever work?


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