Dear Group, is there any package in bioconductor that allows me to apply Fishers exact test on my own annoated categories. I would be using the entire genome or chip as the reference. Thank you. Ad.

Adrian, Would ? fisher.test be helpful? You could also have a look at the Category, GOstats and topGO packages. Adrian Johnson wrote: > Dear Group, > is there any package in bioconductor that allows me to apply Fishers > exact test on my own annoated categories. I would be using the entire > genome or chip as the reference. > Thank you. > Ad. -- Best wishes Wolfgang ------------------------------------------------------- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber

Hi Adrian, One way would be use the Category package to use your own annotations. ?hyperGTest can point you in the right direction, but it's not trivial if you're not familiar with R object-oriented programming. In a hurry, I tend to just code it up myself and feed it through fisher.test. I've been wanting to make hyperGTest work with GSEABase, but haven't had the time to do it yet. Francois Adrian Johnson wrote: > Dear Group, > is there any package in bioconductor that allows me to apply Fishers > exact test on my own annoated categories. I would be using the entire > genome or chip as the reference. > Thank you. > Ad. > > _______________________________________________ > 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