How does the vsn method compare to rma, in terms of bias and the variance between replicates? Has anyone applied both methods to a standard dataset and compared the results? Thanks, Tom Price ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Thomas S. Price Wellcome Trust Training Fellow Wellcome Trust Centre Telephone +44 1865 287608 for Human Genetics, Oxford www.well.ox.ac.uk/~tprice ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Hi Tom, >How does the vsn method compare to rma, in terms of bias and the >variance between replicates? Has anyone applied both methods to a >standard dataset and compared the results? I am not aware of a comprehensive comparison to RMA yet; However: vsn only addresses the aspects "calibration" and "data transformation". The method does not make recommendations on whether to use PM values only or to subtract PM-MM, and on how to calculate the probe set average from the 16 or 20 values for the individual probes. Whereas RMA, as far as I am aware of, does make such recommendations. According to previous postings on this list, Oliver Hartmann is currently working on a comparison on the test data set at http://www.affymetrix.com/analysis/download_center2.affx. I will be highly interested in the results of such comparisons! Best regards Wolfgang Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center (DKFZ) Im Neuenheimer Feld 580 69120 Heidelberg, Germany w.huber@dkfz.de http://www.dkfz.de/abt0840/whuber Tel +49-6221-424709 Fax +49-6221-42524709