[BioC] How do I set the median when performing MAS5.0 normalization

Matthew Willmann willmann at sas.upenn.edu
Mon Dec 6 17:16:31 CET 2010


I am trying to replicate results in a published paper, where they performed a MAS5.0 normalization with the median normalized to 50 and then defined genes as present if the normalized expression value is higher than 30.  Does anyone know how I can alter the standard code to establish these parameters?

> Cel.files=list.files(pattern=".CEL")
> data.MRW=ReadAffy(filenames=Cel.files)
> mas5(data.MRW, normalize=TRUE, sc=500)

Thank you for your time and advice.


Matthew R. Willmann, Ph.D.
Research Associate, Poethig Lab
University of Pennsylvania
Department of Biology
433 S. University Avenue
Philadelphia, PA 19104
Lab phone: 215-898-8916
Cell: 508-243-2495
Fax: 215-898-8780

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