Dear Alyaa, Along the lines of what Paul suggested, you may want to try the GSVA package which offers an entry point for several gene set and pathway summarization methods from microarray and RNA-seq data. Next to that particular statistical functionality you may find also useful in the package the functionality for the non-trivial task of mapping features in ExpressionSet objects to gene sets via the GSEABase package infrastructure. Cheers, Robert. ----- Reply message ----- From: "Alyaa Mahmoud" <alyamahmoud@gmail.com> To: "bioconductor@r-project.org" <bioconductor@r-project.org> Subject: [BioC] correlation between two pathways' genes Date: Sat, Dec 15, 2012 5:13 pm Dear Group I would like to find if the genes of two different pathways are correlated or anti-correlated or no correlation at all. The number of genes in the two pathways are different, that's why a simple scatter plot will not be effective. Is there a simple way I can do this ? Thank you very much Alyaa Mahmoud Jr Computational Biologist Biology Department American University in Cairo, Egypt alya.mahmoud@aucegypt.edu +2 0100 17 31 389 -- Alyaa Mahmoud "Love all, trust a few, do wrong to none"- Shakespeare [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]