Hi, I'm wondering if someone can help me with the result extraction after hyperGTest in GOstats package. After I obtained the hyperGTest result, I also want to know what category each input gene associates with, for example a KEGG pathway. What function should I use? Or should I use another package? Thanks! Chen, Yue This email is intended only for the use of the individua...{{dropped:12}}

Yue, Chen - BMD wrote: > Hi, > > I'm wondering if someone can help me with the result extraction after > hyperGTest in GOstats package. After I obtained the hyperGTest > result, I also want to know what category each input gene associates > with, for example a KEGG pathway. What function should I use? Or > should I use another package? It's not clear what you want here. As Elmar Bucher shows in another email, you can use the KEGG.db package directly to get the information you want. However, this question is reminiscent of a question I have had in the past. Namely, which genes (reporters) are associated with a given GO/KEGG pathway that was found significant in a Fisher's exact test. To answer this question, you want the probeSetSummary() function in the GOstats package. Best, Jim > > Thanks! > > Chen, Yue > > > > This email is intended only for the use of the > individua...{{dropped:12}} > > _______________________________________________ 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues