Question: Fwd: Re: which package can do GSEA for no model organism
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10.3 years ago by
Naomi Altman6.0k
Naomi Altman6.0k wrote:
>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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