[BioC] mas5 question

James W. MacDonald jmacdon at med.umich.edu
Wed Aug 23 17:00:25 CEST 2006

Hi Enrique,

> hi,
> Im doing a mas5 normalization & I have a technical question:
> using mas5() i get the normalization values foreach probeSet foreach
> chip
> using mas5calls() i get PMA calls oreach probeSet foreach chip
> how i can have all in the same file, foreach probeset foreach chip 1
> column of PMA values followed by a column of normalized values?
> (can i use a particular method for that like mas5.detection() or
> mas5calls,AffyBatch-method() or mas5calls,ProbeSet-method() or
> mas5calls.AffyBatch() or mas5calls.ProbeSet() )

affystart(plot=FALSE, express="mas5")

will output a text file formatted just as you request. If you want to do 
anything else with that file, you can read it into R using read.table().



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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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