Entering edit mode
>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