

I am also bit confused that this count step is outside R according to 
the Dexseq manual. I checked the python script, does it request R 
environment? Maybe I am wrong...


On Saturday, November 9, 2013 7:40 AM, Sean Davis <sdavis2@mail.nih.gov> wrote:
 
On Sat, Nov 9, 2013 at 8:34 AM, Simon Anders <anders@embl.de> wrote:

> Hi
>
> On 09/11/13 07:08, capricy gao wrote:
>
>> The problem is our server updates R once a year, I think.
>>
>> How does it affect the results?
>>
>
> Well, without the '-r' option you cannot switch of gene aggregation, which
> may be inconvenient. Also, you may encounter bugs which have already been
> fixed.
>
> Bioinformatics is a fast moving field, and you have to do an effort to
> stay up to date and make sure you always work with current versions of
> tools. Specifically, for the Bioconductor project, it is strongly advised
> to not work with an outdated R version.
>
> Better talk to your sysadmin and ask him/her to update R more frequently.
>

An alternative is to install your own R in your home directory.  No
sysadmin support is necessary to do so and it really isn't that hard (most
of the time).

Sean

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