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

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