Actually, making this question more nontrivial is, 1. the lengths for the two gene lists are very different; 2. I could add another list as gene weight to any gene, for example, of union of two gene lists. On Sun, Aug 24, 2008 at 9:15 AM, Shannon, William <wshannon@dom.wustl.edu>wrote: > First thought is a similarity can be based on the ratio of the number of > genes in the intersection of the two lists divided by the number of genes in > the union of the two lists. If the two lists are identical the similarity > is 1 and if they have no genes in common they have a similarity of 0. Of > course this won't take into account the length of the gene lists. > > You would have to think through what would happen to the similarity for > cases where some genes are in both lists. > > > Bill Shannon > Associate Professor of Biostatistics in Medicine > Washington University School of Medicine > > President-Elect, Classification Society > > ________________________________________ > From: bioconductor-bounces@stat.math.ethz.ch [ > bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Weiwei Shi [ > helprhelp@gmail.com] > Sent: Saturday, August 23, 2008 7:55 PM > To: r-help@stat.math.ethz.ch > Cc: Bioconductor > Subject: [BioC] similarity between two gene lists with varied length > > Dear listers, > > a little off-topic: > > I am looking for and compare algorithms which can calculate "distance" or > "similarity" between two gene lists with different lengths. > > Any paper, any implementation in R and any suggestion is welcome! > > Thanks, > > -- > Weiwei Shi, Ph.D > Research Scientist > GeneGO, Inc. > > "Did you always know?" > "No, I did not. But I believed..." > ---Matrix III > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III [[alternative HTML version deleted]]

>> I am looking for and compare algorithms which can calculate "distance" or >> "similarity" between two gene lists with different lengths. >> >> Any paper, any implementation in R and any suggestion is welcome! > Also, Section 22.4.1. of this book might be of interest: Gentleman R., Carey V., Huber W., Irizarry R. and Dudoit S. (2005) Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Published by Springer. Best wishes Wolfgang -- ---------------------------------------------------- Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber