[BioC] Dexseq package: dexseq_count error message and warnings

[Alejandro Reyes]

Dear Capricy,

The python scripts does not require an R environment.
If you install an updated version of R and DEXSeq, you will find an 
example of how to do this preprocessing steps within R in the Appendix 
section.

Best regards,
Alejandro

>
>
> 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 at mail.nih.gov> wrote:
>
> On Sat, Nov 9, 2013 at 8:34 AM, Simon Anders <anders at 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 to not work with an outdated R version.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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