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

[Naomi Altman]

>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
>>
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>
>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