[Bioperl-l] The Power of R

[Chris Fields]

The current preliminary BioC interface in biolib is actually a direct  
swig-based interface to the affyio C lib in BioC.  It should be a much  
faster solution (i.e. you shouldn't have to go Perl<->R<->affyio, but  
Perl<->affyio).  Pjotr has indicated more swig-based interfaces are  
possibly on the way.

chris

On Jan 7, 2009, at 9:32 AM, Dr. T. I. Simpson wrote:

> I did use RSPerl but was deeply displeased with what was simply a  
> solution born of necessity at the time. It got the job done, but was  
> not a long term solution. I look likely to revisit the throny issue  
> in the next couple of months as I am trying to package up some  
> simple downstream clustering analysis code into a bioperl package. I  
> would dearly love to have it all nicely connected up to R, so am  
> keeping an eye on the some threads that are running on BioC/BioPerl  
> integration and the potential to use BioLib for this purpose http://biolib.open-bio.org/wiki/Main_Page 
> . I know painfully little about this at the moment, but plan to gen  
> up in the coming weeks.
>
> Ian.
>
> On Wed, 07 Jan 2009 15:19:44 -0000, Mark A. Jensen  
> <maj at fortinbras.us> wrote:
>
>> What solution did you responders wind up using? Do people generally  
>> get RSPerl to work and wash their hands of it afterwards? Or do you  
>> finally hand-code a good deal? thx
>> ----- Original Message ----- From: "Dr. T. I. Simpson" <ian.simpson at ed.ac.uk 
>> >
>> To: "Chris Fields" <cjfields at illinois.edu>; "Boris Umylny" <umylny at apbri.org 
>> >
>> Cc: <bioperl-l at lists.open-bio.org>
>> Sent: Wednesday, January 07, 2009 9:55 AM
>> Subject: Re: [Bioperl-l] The Power of R
>>
>>
>>> I agree with Chris on this.
>>>
>>> Used RSPerl about a year ago to integrate some clustering  
>>> experiments in R with a Perl script that fed data to R and picked  
>>> up output, but it was  mighty painful and accessing R objects  
>>> through RSPerl was indeed a PITA.
>>>
>>> Ian.
>>>
>>>
>>> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields <cjfields at illinois.edu 
>>> > wrote:
>>>
>>>> Not to bash this, as it is a decent piece of software, but...  : >
>>>>
>>>> 1) Painful to install, and doesn't support a local perl  
>>>> installation  (keeps attempting to go back and use my 5.8.8  
>>>> instead of my local 5.10).
>>>> 2) Not on CPAN.
>>>> 3) Though this is supposed to be bidirectional, R from Perl is  
>>>> not well supported and apparently does not work for Windows.
>>>> 4) Doesn't appear to be well-supported in general.
>>>>
>>>> I do not intend on writing a full perl suite for R/BioC analyses  
>>>> if I  end up having to work around problems with the critical  
>>>> module.
>>>>
>>>> -c
>>>>
>>>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote:
>>>>
>>>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)?
>>>>>
>>>>>
>>>>> Boris
>>>>>
>>>>>
>>>>> ----- Original Message ----- From: "Chris Fields" <cjfields at illinois.edu
>>>>> >
>>>>> To: "Mark A. Jensen" <maj at fortinbras.us>
>>>>> Cc: <bioperl-l at lists.open-bio.org>
>>>>> Sent: Wednesday, January 07, 2009 2:04 PM
>>>>> Subject: Re: [Bioperl-l] The Power of R
>>>>>
>>>>>
>>>>>> Now if we can only get a decent Perl-R interface which isn't a  
>>>>>> PITA to install...
>>>>>>
>>>>>> chris
>>>>>>
>>>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote:
>>>>>>
>>>>>>> So says the New York Times:
>>>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html
>>>>>>>
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>>>
>>>
>>>
>>> -- Dr T. I. Simpson
>>> School of Biomedical Sciences
>>> University of Edinburgh
>>> Hugh Robson Building
>>> George Square
>>> Edinburgh
>>> EH8 9XD
>>>
>>> ian.simpson at ed.ac.uk
>>>
>>>
>>> The University of Edinburgh is a charitable body, registered in
>>> Scotland, with registration number SC005336.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>
>>
>
>
>
> -- 
> Dr T. I. Simpson
> School of Biomedical Sciences
> University of Edinburgh
> Hugh Robson Building
> George Square
> Edinburgh
> EH8 9XD
>
> ian.simpson at ed.ac.uk
>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.