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 ? 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.

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