Question: Fwd: Re: which package can do GSEA for no model organism
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gravatar for Pengcheng Yang
10.2 years ago by
Pengcheng Yang40 wrote:
Hi Marc, We are working on Locust (Locusta Migratoria). Marc Carlson ??: > 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 >> > > _______________________________________________ > 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 > > -- Pengcheng Yang PhD Candidate IOZ,CAS email: <yangpc at="" ioz.ac.cn="">
ADD COMMENTlink written 10.2 years ago by Pengcheng Yang40
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