Hi, I'm wondering if there is a package for GO enrichment analysis in multiple Groups? For example, I have array data from 5 different tissues and would like to find the enriched GO categories in one group compared to all the other 4 groups. Thanks for your help. Mingqian Huang MEEI

Hi, Mingqian This function will be added in the dev version of GeneAnswers. So far, you can use getEnrichmentInfo() to retrieve the enrichmentINfo and make a multiple gene concept table by yourself. Actually, the basic function is ready and we are working on integrate it into our package. Hope this is helpful for you! Gilbert On 12/18/09 10:34 AM, "M.H." <huangva at="" gmail.com=""> wrote: > Hi, > > I'm wondering if there is a package for GO enrichment analysis in multiple > Groups? For example, I have array data from 5 different tissues and would > like to find the enriched GO categories in one group compared to all the > other 4 groups. Thanks for your help. > > Mingqian Huang > MEEI > > _______________________________________________ > 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 > ----------------------------------------------- Gang (Gilbert) Feng, PhD Biomedical Informatics Center Robert H. Lurie Comprehensive Cancer Center Northwestern University 750 N. Lake Shore Drive, 11th Floor(11-175e) Chicago, IL 60611 Phone:312-503-2358 Email g-feng (at) northwestern.edu

Hi Mingqian, you could also use the Category package (start by looking at its vignette "Using Categories to Model Genomic Data"), which allows you to define any statistic that you care about (such as an F-statistic, or the contrast from a linear model) and check for gene sets (GO categories) correlated with this statistic. Best wishes Wolfgang M.H. scripsit 12/18/2009 05:34 PM: > Hi, > > I'm wondering if there is a package for GO enrichment analysis in multiple > Groups? For example, I have array data from 5 different tissues and would > like to find the enriched GO categories in one group compared to all the > other 4 groups. Thanks for your help. > > Mingqian Huang > MEEI > > _______________________________________________ > 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 -- Best wishes Wolfgang -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact