Hi Weiwei, You may want to have a look at the Bioconductor package OrderedList. It searches for similarities in gene rankings without forcing the user to specify a threshold, where to cut the lists. Hope this helps, Cheers, Claudio -----Original Message----- From: "Weiwei Shi" [mailto:helprhelp@gmail.com] Sent: Sunday, August 24, 2008 2:56 AM To: "r-help at stat.math.ethz.ch" <r-help at="" stat.math.ethz.ch=""> Cc: Bioconductor <bioconductor at="" stat.math.ethz.ch=""> 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 at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

The made4 package in bioconductor can report gene list similarities. --- Deanne Taylor PhD Executive Director, Bioinformatics Core Department of Biostatistics Harvard School of Public Health 655 Huntington Avenue Boston, MA 02115 dtaylor at hsph.harvard.edu >>> "Weiwei Shi" <helprhelp at="" gmail.com=""> 08/23/08 8:59 PM >>> 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 at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor