Hi All, Can any one suggest me the procedure/software to conduct Hypergeometric test on my gene list? I have a list of deferentially regulated genes and list of sets of genes involved in common biological process , function and cellular component. I have done part of it using BINGO and DAVID but I need to perform this on my own gene set that I have made in a way to answer my specific research question. Thanks Amit -- [[alternative HTML version deleted]]

Hi, On Thu, Nov 21, 2013 at 12:53 AM, amit kumar subudhi <amit4help at="" gmail.com=""> wrote: > Hi All, > > Can any one suggest me the procedure/software to conduct Hypergeometric > test on my gene list? I have a list of deferentially regulated genes and > list of sets of genes involved in common biological process , function and > cellular component. > I have done part of it using BINGO and DAVID but I need to perform this on > my own gene set that I have made in a way to answer my specific research > question. The GOstats package can help you here: http://www.bioconductor.org/packages/2.13/bioc/html/GOstats.html You could either go "whole hog" and follow the instructions in the "Hypergeometric tests for less common model organisms" vignette, or simply just rig up your own hyper-geometric tests in a more "manual" way via the `phyper` function. If you browse through the source of the "Hypergeometric Tests Using GOstats" vignette there, you will even see a small function that shows you how to use it, the relevant bits being: phyper(numFound-1, numAtCat, numNotAtCat, numDrawn, lower.tail=FALSE) The var names used here combined with the help in ?phyper should get you where you need to go. HTH, -steve -- Steve Lianoglou Computational Biologist Genentech