[BioC] Fwd: Re: which package can do GSEA for no model organism
Ian Sudbery
ims at sanger.ac.uk
Tue Jun 30 10:56:31 CEST 2009
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
>>>>
>>>> _______________________________________________
>>>> 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.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 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
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
More information about the Bioconductor
mailing list