[BioC] Quality of Affy Chips with the affy package

Oliver Hartmann hartmann@mailer.uni-marburg.de
Thu, 13 Feb 2003 17:58:39 +0100

Dear list members,

in chapter 4 of "Textual description of affy" several methods for 
quality control are described: hist(), image(), boxplot() and RNA 
degradation plots.

Has anybody used these methods to identify bad quality chips? When do 
you exclude a chip from further analysis? What's your decision rule?
Any other suggestions on how to identify bad quality from the data alone?

Thanks a lot.

Oliver Hartmann, Institute of Medical Biometry and Epidemiology
Philipps-University Marburg, Bunsenstr. 3, D-35037 Marburg
phone +49(0)6421 28 66514, fax +49(0)6421 28 68921