[BioC] Quality of Affy Chips with the affy package

Zhang, Xueqing Xueqing.Zhang@umassmed.edu
Thu, 13 Feb 2003 12:24:37 -0500

A lot of target sequences are very short and just in 3'UTR, does RNA degradation plot really show overall degradation? 

-----Original Message-----
From: Oliver Hartmann [mailto:hartmann@mailer.uni-marburg.de]
Sent: Thursday, February 13, 2003 11:59 AM
To: bioconductor@stat.math.ethz.ch
Subject: [BioC] Quality of Affy Chips with the affy package

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

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