[BioC] plotting GO output as pie charts

[Dick Beyer]

>
> Hi everybody,
> I was wondering if there was a simple function allowing me to do this,
> plotting a GO-output search from ensembl into a pie-chart?
> I looked at biomaRt but the main problem I'm facing here is actually
> calling ensembl database as my Institute doesn't allow me to do so
> through R (I'm working on a farm nodes Linux 64), but also I couldn't
> actually find anywhere such a function in the package.
> So I took out my list of Human affyID I'm interested in, and used
> biomart directly on the web of Ensembl to fetch all the GO IDs
> associated... Now I'd like to plot those, and preferentially in a "user
> defined" fashion (by selecting the GO categories I want my genes to
> separate into, the end idea would be to compare several lists, for the
> same categories...)
>
> Thank you for your help
> Celine
>
> --
> ----------------------------------------------------
> Celine Carret PhD
> Pathogen Microarrays group
> The Wellcome Trust Sanger Institute
> Hinxton, Cambridge CB10 1SA, UK.
> tel. +44 (0)1223 494 940
> fax. +44 (0)1223 494 919
> email: ckc at sanger.ac.uk
> http://www.sanger.ac.uk/PostGenomics/PathogenArrays/
>

Hi Celine,

Check out ontoCompare in the goTools package.  It might be what you are looking for.

Cheers,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer
*******************************************************************************

  ------------------------------
>
> Message: 2
> Date: Mon, 22 May 2006 17:07:26 +0100
> From: Celine Carret <ckc at sanger.ac.uk>
> Subject: [BioC] plotting GO output as pie charts
> To: bioconductor at stat.math.ethz.ch, Wolfgang Huber <huber at ebi.ac.uk>
> Message-ID: <4471E1BE.1010006 at sanger.ac.uk>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> Hi everybody,
> I was wondering if there was a simple function allowing me to do this,
> plotting a GO-output search from ensembl into a pie-chart?
> I looked at biomaRt but the main problem I'm facing here is actually
> calling ensembl database as my Institute doesn't allow me to do so
> through R (I'm working on a farm nodes Linux 64), but also I couldn't
> actually find anywhere such a function in the package.
> So I took out my list of Human affyID I'm interested in, and used
> biomart directly on the web of Ensembl to fetch all the GO IDs
> associated... Now I'd like to plot those, and preferentially in a "user
> defined" fashion (by selecting the GO categories I want my genes to
> separate into, the end idea would be to compare several lists, for the
> same categories...)
>
> Thank you for your help
> Celine
>
> --
> ----------------------------------------------------
> Celine Carret PhD
> Pathogen Microarrays group
> The Wellcome Trust Sanger Institute
> Hinxton, Cambridge CB10 1SA, UK.
> tel. +44 (0)1223 494 940
> fax. +44 (0)1223 494 919
> email: ckc at sanger.ac.uk
> http://www.sanger.ac.uk/PostGenomics/PathogenArrays/
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 22 May 2006 12:34:43 -0400
> From: Sean Davis <sdavis2 at mail.nih.gov>
> Subject: Re: [BioC] plotting GO output as pie charts
> To: Celine Carret <ckc at sanger.ac.uk>,	Bioconductor
> 	<bioconductor at stat.math.ethz.ch>,	Wolfgang Huber <huber at ebi.ac.uk>
> Message-ID: <C0976063.BD51%sdavis2 at mail.nih.gov>
> Content-Type: text/plain;	charset="US-ASCII"
>
>
>
>
> On 5/22/06 12:07 PM, "Celine Carret" <ckc at sanger.ac.uk> wrote:
>
>> Hi everybody,
>> I was wondering if there was a simple function allowing me to do this,
>> plotting a GO-output search from ensembl into a pie-chart?
>> I looked at biomaRt but the main problem I'm facing here is actually
>> calling ensembl database as my Institute doesn't allow me to do so
>> through R (I'm working on a farm nodes Linux 64), but also I couldn't
>> actually find anywhere such a function in the package.
>> So I took out my list of Human affyID I'm interested in, and used
>> biomart directly on the web of Ensembl to fetch all the GO IDs
>> associated... Now I'd like to plot those, and preferentially in a "user
>> defined" fashion (by selecting the GO categories I want my genes to
>> separate into, the end idea would be to compare several lists, for the
>> same categories...)
>
> You may want to look at the GOstats, GO, Category, and annotate packages in
> bioconductor.  Affy gets a great deal of "special treatment" in the
> microarray community because of its popularity; Bioconductor includes the
> annotation packages for most of the affy arrays and these annotation
> packages typically have GO mappings.  The R function pie() makes pie charts.
>
> Sean
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 22 May 2006 16:30:41 -0700
> From: Kasper Daniel Hansen <khansen at stat.Berkeley.EDU>
> Subject: Re: [BioC] Affy's .DTT format?
> To: Jenny Drnevich <drnevich at uiuc.edu>
> Cc: bioconductor at stat.math.ethz.ch
> Message-ID: <D84C281E-FE92-418E-8008-3D46E9290918 at stat.berkeley.edu>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> On May 22, 2006, at 8:56 AM, Jenny Drnevich wrote:
>
>> Hi everyone,
>>
>> Our core facility was told by our Affy rep they should switch to
>> the .DTT
>> flat archive file instead of the CAB format as the way to store
>> data and to
>> disseminate it to researchers. However, this file format is basically
>> useless right now without Affy's Data Transfer Tool and GCOS
>> software; to
>> get the .CEL files, I had to use the Data Transfer Tool to import
>> the .DTT
>> file into my local GCOS database, then use it again to export the
>> flat .CEL
>> files.  I've talked with our core, and instead they are going to
>> give out
>> the .CEL, .CHP and .DAT flat files, at least for now. I noticed
>> that Affy
>> does have a DTT SDK, and wondered if anyone within Bioconductor was
>> planning on/working on being to import data from the .DTT format?
>> I'm not
>> sure what our rep was thinking, because I don't think any analysis
>> software
>> out there can take .DTT files (yet?).
>
> Hi Jenny
>
> The SDK we are interfacing to in affxparser contains methods for
> parsing DTT files. I did not really know of this format until this
> morning, and I am still trying to figure out whether it really makes
> sense to support. Basically it seems like a way to bundle cel, chp
> and dat files, and stuff I have read on the Affy website seems to
> indicate that it primarily makes sense for people wanting to share
> _all_ data and subsequently use it in some of Affy's own software.
> Eg. they provide both "flat" cel files and dtt-bundled cel files for
> some of their SNP data. It also seems like there exists both a dtt
> format and a "flat" dtt format - whatever the difference is. I will
> try to investigate a bit (and if you hear something please write).
>
> Adding support for the DTT file to affxparser would be "simple" but
> probably take considerable time since that part of the SDK depends on
> external libraries we would then have to figure out how to deploy
> etc. My first impression is that it is not worth the effort to do
> this (unless we are forced :)
>
> My final verdict will depend on my investigation, and - of course -
> whether there is a large interest in this...
>
> /Kasper
>
>> Cheers,
>> Jenny
>>
>> Jenny Drnevich, Ph.D.
>>
>> Functional Genomics Bioinformatics Specialist
>> W.M. Keck Center for Comparative and Functional Genomics
>> Roy J. Carver Biotechnology Center
>> University of Illinois, Urbana-Champaign
>>
>> 330 ERML
>> 1201 W. Gregory Dr.
>> Urbana, IL 61801
>> USA
>>
>> ph: 217-244-7355
>> fax: 217-265-5066
>> e-mail: drnevich at uiuc.edu
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/
>> gmane.science.biology.informatics.conductor
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 22 May 2006 22:27:37 -0700
> From: Kasper Daniel Hansen <khansen at stat.Berkeley.EDU>
> Subject: Re: [BioC] Affy's .DTT format?
> To: Kasper Daniel Hansen <khansen at stat.Berkeley.EDU>
> Cc: bioconductor List <bioconductor at stat.math.ethz.ch>
> Message-ID: <2A5FFBCA-BC08-40A4-8E43-48E18750351F at stat.berkeley.edu>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
>
> On May 22, 2006, at 4:30 PM, Kasper Daniel Hansen wrote:
>
>> On May 22, 2006, at 8:56 AM, Jenny Drnevich wrote:
>>
>>> Hi everyone,
>>>
>>> Our core facility was told by our Affy rep they should switch to
>>> the .DTT
>>> flat archive file instead of the CAB format as the way to store
>>> data and to
>>> disseminate it to researchers. However, this file format is basically
>>> useless right now without Affy's Data Transfer Tool and GCOS
>>> software; to
>>> get the .CEL files, I had to use the Data Transfer Tool to import
>>> the .DTT
>>> file into my local GCOS database, then use it again to export the
>>> flat .CEL
>>> files.  I've talked with our core, and instead they are going to
>>> give out
>>> the .CEL, .CHP and .DAT flat files, at least for now. I noticed
>>> that Affy
>>> does have a DTT SDK, and wondered if anyone within Bioconductor was
>>> planning on/working on being to import data from the .DTT format?
>>> I'm not
>>> sure what our rep was thinking, because I don't think any analysis
>>> software
>>> out there can take .DTT files (yet?).
>>
>> Hi Jenny
>>
>> The SDK we are interfacing to in affxparser contains methods for
>> parsing DTT files. I did not really know of this format until this
>> morning, and I am still trying to figure out whether it really makes
>> sense to support. Basically it seems like a way to bundle cel, chp
>> and dat files, and stuff I have read on the Affy website seems to
>> indicate that it primarily makes sense for people wanting to share
>> _all_ data and subsequently use it in some of Affy's own software.
>> Eg. they provide both "flat" cel files and dtt-bundled cel files for
>> some of their SNP data. It also seems like there exists both a dtt
>> format and a "flat" dtt format - whatever the difference is. I will
>> try to investigate a bit (and if you hear something please write).
>>
>> Adding support for the DTT file to affxparser would be "simple" but
>> probably take considerable time since that part of the SDK depends on
>> external libraries we would then have to figure out how to deploy
>> etc. My first impression is that it is not worth the effort to do
>> this (unless we are forced :)
>>
>> My final verdict will depend on my investigation, and - of course -
>> whether there is a large interest in this...
>
> Some investigation and an email to devnet at affy uncovered that the big
> DTT bundle is in fact just a zip file containing EXP, CEL and CHP
> files for each array. There seems to be an extra base file containing
> the CDF file. DAT files are not included.
>
> The DTT format I was referring to is an XML based format describing
> some details about the experiment in a MAGEML (like) structure.
>
> So I will not do anything about adding parsing capability - just use
> your favorite zip program. It is not worth the time and effort to
> parse DTT files using the SDK.
>
> As a small curiosity, some of the DTT files for the 100k snp arrays
> available on Affy's site are corrupted - look at the 500k instead.
>
> /Kasper
>
>> /Kasper
>>
>>> Cheers,
>>> Jenny
>>>
>>> Jenny Drnevich, Ph.D.
>>>
>>> Functional Genomics Bioinformatics Specialist
>>> W.M. Keck Center for Comparative and Functional Genomics
>>> Roy J. Carver Biotechnology Center
>>> University of Illinois, Urbana-Champaign
>>>
>>> 330 ERML
>>> 1201 W. Gregory Dr.
>>> Urbana, IL 61801
>>> USA
>>>
>>> ph: 217-244-7355
>>> fax: 217-265-5066
>>> e-mail: drnevich at uiuc.edu
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/
>>> gmane.science.biology.informatics.conductor
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/
>> gmane.science.biology.informatics.conductor
>
>
>
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>
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