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 Investigaci?n Pr?ncipe 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.

Hi Pengcheng, What organism are you working on? Marc 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 Investigaci?n Pr?ncipe 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