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@stat.psu.edu
>> Para: bioconductor@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@ioz.ac.cn>
>>>> From: Naomi Altman <naomi@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@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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor@stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/gmane.science.biology.inf
>>>       
>> ormatics.conductor
>>     
>
> -------------------------------------------
> Ana Conesa, PhD
> Bioinformatics Department
> Centro de Investigación Príncipe Felipe
> Avda. Autopista Saler 16
> 46013 Valencia Spain
> http://bioinfo.cipf.es/aconesa
> ===========================================
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>   


-- 
Pengcheng Yang
PhD Candidate
IOZ,CAS
email: <yangpc@ioz.ac.cn>


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