[BioC] vsn / rma

[Wolfgang Huber]

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