I have done the analysis with DAVID but someone told me to do this kind of analysis. because he believes that if i randomly select 185 others genes among the 6000 i will have the same annotation results .... > Date: Mon, 4 Jun 2012 09:14:13 -0400 > Subject: Re: [BioC] Gene list annotation > From: sdavis2@mail.nih.gov > To: guest@bioconductor.org > CC: bioconductor@r-project.org; flower_des_iles@hotmail.com > > On Mon, Jun 4, 2012 at 9:09 AM, Fleur [guest] <guest@bioconductor.org> wrote: > > > > Hi, > > I'm trying to measure the significance of my gene annotation list. > > Gene list of interest is composed of 185 genes ( among 6000 genes).In a first step, i performed a GO term analysis but i would like to know if i could have the same result by chance. > > My idea was to randomly select 185 genes from the 6000 genes ( 100 times for example) and annotate those list and see if i could have the same terms by chance ... But how calculate a pvalue for each term at each repetition of the permutation ? Any idea ? > > Someone know a package which do this king of thing ? > > GOstats, topGo, limma (roast, romer, and friends), and several others > might be applicable. You mentioned that you had done a "GO term > analysis", so you may have already done this, depending on what you > meant by that statement. > > Sean > > > > Thanks in advance for your help > > > > > > > > > > -- output of sessionInfo(): > > > > R version 2.13.0 (2011-04-13) > > Platform: i386-pc-mingw32/i386 (32-bit) > > > > locale: > > [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 > > [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C > > [5] LC_TIME=French_France.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

On Mon, Jun 4, 2012 at 9:50 AM, St?phanie haaaaaaaa <flower_des_iles at="" hotmail.com=""> wrote: > > I have done the analysis with DAVID but someone told me to do this kind of analysis. because he believes that if i randomly select 185 others genes among the 6000 i will have the same annotation results .... > DAVID uses a fisher-exact-based statistic for computing the probability of enrichment. Did you get p-values from DAVID? If so, you may have already accomplished your task. If not, you can use DAVID to get such a result, but that is for another list.... Sean >> Date: Mon, 4 Jun 2012 09:14:13 -0400 >> Subject: Re: [BioC] Gene list annotation >> From: sdavis2 at mail.nih.gov >> To: guest at bioconductor.org >> CC: bioconductor at r-project.org; flower_des_iles at hotmail.com >> >> On Mon, Jun 4, 2012 at 9:09 AM, Fleur [guest] <guest at="" bioconductor.org=""> wrote: >> > >> > Hi, >> > I'm trying to measure the significance of my gene annotation list. >> > Gene list of interest is composed of 185 genes ( among 6000 genes).In a first step, i performed a GO term analysis but i would like to know if i could have the same result by chance. >> > My idea was to randomly select 185 genes from the 6000 genes ( 100 times for example) and annotate those list and see if i could have the same terms by chance ... But how calculate a pvalue for each term at each repetition of the permutation ? Any idea ? >> > Someone know a package which do this king of thing ? >> >> GOstats, topGo, limma (roast, romer, and friends), and several others >> might be applicable. ?You mentioned that you had done a "GO term >> analysis", so you may have already done this, depending on what you >> meant by that statement. >> >> Sean >> >> >> > Thanks in advance for your help >> > >> > >> > >> > >> > ?-- output of sessionInfo(): >> > >> > R version 2.13.0 (2011-04-13) >> > Platform: i386-pc-mingw32/i386 (32-bit) >> > >> > locale: >> > [1] LC_COLLATE=French_France.1252 ?LC_CTYPE=French_France.1252 >> > [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C >> > [5] LC_TIME=French_France.1252 >> > >> > attached base packages: >> > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> > >> > -- >> > Sent via the guest posting facility at bioconductor.org. >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor