Hi all, I wanted to ask if someone could give me a little overview of the options I have if I want to determine clusters of correlated genes in expression data. I have found several useful functions, but as usual, no matter how hard I look, I am sure I am missing half of the options available. Thanks! Kamila

I recommend that you check out Steve Horvath's work (UCLA) [1]http://www.genetics.ucla.edu/labs/horvath/ModuleConformity/ [2]http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/ if you have not done so already. Cheers Carleton T. Garrett -----bioconductor-bounces at stat.math.ethz.ch wrote: ----- To: bioconductor at stat.math.ethz.ch From: knaxerov at ix.urz.uni-heidelberg.de Sent by: bioconductor-bounces at stat.math.ethz.ch Date: 03/19/2007 10:47AM Subject: [BioC] methods for determining clusters of correlated genes Hi all, I wanted to ask if someone could give me a little overview of the options I have if I want to determine clusters of correlated genes in expression data. I have found several useful functions, but as usual, no matter how hard I look, I am sure I am missing half of the options available. Thanks! Kamila _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch [3]https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: [4]http://news.gmane.org/gmane.science.biology.informatics.conducto r NOTE: The information contained in this message may be privileged and confidential and protected from disclosure. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately by replying to the message and deleting it from your computer. -------------------------------------- VCU Health System http://www.vcuhealth.org References 1. http://www.genetics.ucla.edu/labs/horvath/ModuleConformity/ 2. http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/ 3. https://stat.ethz.ch/mailman/listinfo/bioconductor 4. http://news.gmane.org/gmane.science.biology.informatics.conductor

Dear Kamila, The possibilities are infinite, I don't think it is possible or useful to provide an exhaustive overview. Anyway, we have tried to give a basic view in a chapter on clustering this book: Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Series: Statistics for Biology and Health Gentleman, R.; Carey, V.; Huber, W.; Irizarry, R.; Dudoit, S. (Eds.) 2005, 473 p., 128 illus., 128 in colour, Hardcover ISBN: 978-0-387-25146-2 and there are also many good reviews by other authors. Best wishes Wolfgang knaxerov at ix.urz.uni-heidelberg.de wrote: > Hi all, > > I wanted to ask if someone could give me a little overview of the > options I have if I want to determine clusters of correlated genes in > expression data. I have found several useful functions, but as usual, > no matter how hard I look, I am sure I am missing half of the options > available. > > Thanks! > Kamila