[BioC] Fwd: Re: which package can do GSEA for no model organism

[Ian Sudbery]

Have you tried R-GSEA at
http://www.broad.mit.edu/gsea/
which allows the use of standard or custom arrays  and gene sets.

Ian
---


Pengcheng Yang wrote:
> Hi,
> Thanks for your zealous reply.
> Sorry for my inadequate question description.
> We have done the GO annotation for the Unigenes using interproscan. I 
> have written several R functions to do GO/KEGG enrichment analysis for 
> our customized array based on the fisher-exact test and chi-square test. 
> But the analysis is limited to the third level of GO hierarchy. More R 
> functions are needed if I do GSEA at deeper level. So I wonder that why 
> "AnnotationDbi" package or "Category" do not develop a function to 
> create customized annotation packages or objects. The packages/objects 
> contain the annotations of the specific species' Unigenes or other 
> sequences from unsequenced organisms. The annotation contain user 
> defined classes, such as GO, KEGG, IPR, etc. Once the packages/objects 
> is created the GSEA can be done through existed packages,  such as 
> GOstats, topGO, etc.
>
> Thanks, Ana. FatiGO++ really can do the work, but we need run in batch. 
> So program is need.
>
>
>
>
> Ana Conesa ??:
>   
>> Hi
>>
>> You can do GSEA with FatiScan (www.babelomics.org) with any
>> annotation file provided by the user. If you do not have the
>> annotation  for your non-model species you can generate it yourself
>> with Blast2GO (www.blast2go.org) provided you have sequence data, or
>> try to fetch them from the B2G-FAR (www.blast2go.org) site which
>> contains annotation data for over 2000 species, of course, most
>> non-model.
>>
>> Hope this is of use to you
>>
>> Ana
>>
>>
>>   
>>     
>>> ---- Mensaje Original ----
>>> De: naomi at stat.psu.edu
>>> Para: bioconductor at stat.math.ethz.ch
>>> Asunto: RE: [BioC] Fwd: Re:  which package can do GSEA for no model
>>> organism
>>> Fecha: Mon, 29 Jun 2009 13:06:40 -0400
>>>
>>>     
>>>       
>>>>> To: Pengcheng Yang <yangpc at ioz.ac.cn>
>>>>> From: Naomi Altman <naomi at stat.psu.edu>
>>>>> Subject: Re: [BioC] which package can do GSEA for no model organism
>>>>> Cc:
>>>>> Bcc:
>>>>> X-Eudora-Signature: <work>
>>>>> Date: Mon, 29 Jun 2009 13:06:22 -0400
>>>>>
>>>>> Dear Pengcheng,
>>>>> You cannot really talk about enrichment unless you have categories 
>>>>> for your genes.
>>>>>
>>>>> Usually, we use a program such as BLAST to align the unigenes to
>>>>>         
>>>>>           
>>> the 
>>>     
>>>       
>>>>> nearest model organism,
>>>>> and assign GO categories to the best hit.  But this may leave you 
>>>>> with 3 problems - 1) there will be lots of
>>>>> unigenes with no hit  2) there are usually several genes in the 
>>>>> model organism with multiple hits  3) until functional studies are 
>>>>> available for your organism, you can never know if the gene has the
>>>>>         
>>>>> same function in your organism and the model organism.
>>>>>
>>>>> --Naomi
>>>>>
>>>>> At 07:20 AM 6/29/2009, you wrote:
>>>>>         
>>>>>           
>>>>>> Hi,
>>>>>> As far as I know, currently, GO analysis packages are based on
>>>>>> commercial platforms. How can I do GSEA analysis for the
>>>>>>           
>>>>>>             
>>> customized
>>>     
>>>       
>>>>>> array of no model organisms using existed packages? For example,
>>>>>>           
>>>>>>             
>>> an
>>>     
>>>       
>>>>>> array constructed based on unigenes, and the organism's genome has
>>>>>>           
>>>>>>             
>>> not
>>>     
>>>       
>>>>>> yet been sequenced.
>>>>>>
>>>>>> Regards
>>>>>>
>>>>>> --
>>>>>> Pengcheng Yang
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>>>           
>>>>>>             
>>>>> Naomi S. Altman                                814-865-3791 (voice)
>>>>> Associate Professor
>>>>> Dept. of Statistics                              814-863-7114 (fax)
>>>>> Penn State University                         814-865-1348
>>>>>         
>>>>>           
>>> (Statistics)
>>>     
>>>       
>>>>> University Park, PA 16802-2111
>>>>>         
>>>>>           
>>>> Naomi S. Altman                                814-865-3791 (voice)
>>>> Associate Professor
>>>> Dept. of Statistics                              814-863-7114 (fax)
>>>> Penn State University                         814-865-1348
>>>>       
>>>>         
>>> (Statistics)
>>>     
>>>       
>>>> University Park, PA 16802-2111
>>>>
>>>> _______________________________________________
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>>>>       
>>>>         
>>> ormatics.conductor
>>>     
>>>       
>> -------------------------------------------
>> Ana Conesa, PhD
>> Bioinformatics Department
>> Centro de Investigación Príncipe Felipe
>> Avda. Autopista Saler 16
>> 46013 Valencia Spain
>> http://bioinfo.cipf.es/aconesa
>> ===========================================
>>
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>>
>>   
>>     
>
>
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