[BioC] (no subject)

James MacDonald jmacdon at med.umich.edu
Thu Aug 28 11:41:28 MEST 2003

Technical details of how background is calculated can be found on Rafael Irizarry's website


Background is not stored in the affybatch object. It is simply calculated (using PM data) and subtracted from the PM data when you run rma (or expresso, if you accept the default bg.correct-TRUE). Note this is not true if you use bg.correct.method="MAS".

The new background correction method (gcrma) does use MM probes. Info can also be found on the website.


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

>>> Marcus <marcusb at biotech.kth.se> 08/28/03 06:58AM >>>
Hello all!

First of all I would like to thank everybody for a great mailing list, it 
has halped me a lot.

Question: How is the background calculated and how is it stored in my 
affybatch object?
Is it derived from the mm values or does it originate from other data?

Best regards


Marcus Gry Björklund

Royal Institute of Technology
AlbaNova University Center
Stockholm Center for Physics, Astronomy and Biotechnology
Department of Molecular Biotechnology
106 91 Stockholm, Sweden

Phone (office): +46 8 553 783 39
Fax: + 46 8 553 784 81
Visiting adress: Roslagstullsbacken 21, Floor 3
Delivery adress: Roslagsvägen 30B

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