I am thinking of using GOseq to obtain enriched GO terms for RNA-Seq clustering results. I plan to transform the RNA-Seq data before running clustering to make it homoskedastic. When running GOseq, I would provide the list of genes that cluster together as the list of "DE genes". Question: Is this an appropriate usage of GOseq? Or can/should I just use a standard Fisher's Exact Test? Thanks, Julie Julie Leonard Computational Biologist Syngenta Biotechnology Inc. (919) 281-7449 julie.leonard@syngenta.com This message may contain confidential information. If yo...{{dropped:7}}

Hi Julie, In theory you can get your list of "DE" genes any way you like before using Goseq. The issue however for GOseq is that usually when you perform a statistical test for DE it is biased towards long and highly expressed genes. I'm not exactly sure how these features will effect clustering but if you see a trend when calculating nullp() then it's probably worth using Goseq to correct your GO testing for biases. Cheers, Alicia On 18/04/12 8:00 PM, "bioconductor-request at r-project.org" <bioconductor-request at="" r-project.org=""> wrote: > From: <julie.leonard at="" syngenta.com=""> > To: <bioconductor at="" r-project.org=""> > Subject: [BioC] GOseq for enrichment of clustering results > Message-ID: > <e6e983882972d447af74d38898c199631291e2f968 at="" usetcmsxmb02.nafta.syngenta.org=""> > > Content-Type: text/plain > > I am thinking of using GOseq to obtain enriched GO terms for RNA-Seq > clustering results. I plan to transform the RNA-Seq data before running > clustering to make it homoskedastic. When running GOseq, I would provide the > list of genes that cluster together as the list of "DE genes". > > Question: Is this an appropriate usage of GOseq? Or can/should I just use a > standard Fisher's Exact Test? > > Thanks, > Julie > > Julie Leonard > Computational Biologist > Syngenta Biotechnology Inc. > (919) 281-7449 > julie.leonard at syngenta.com > ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com