[Bioperl-l] The Power of R

Wed Jan 7 17:41:22 UTC 2009

On Wed, Jan 7, 2009 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:

> 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.

If affy is what you are after, Affy has their SDK that could potentially be
used directly, though I haven't tried this myself.

Sean

>
>
> 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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>>>>>>>>
>>>>>>>
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>>>>>>
>>>>>>
>>>>> _______________________________________________
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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.
>>
>
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