[BioC] Quality of Affy Chips with the affy package

[Stephen Henderson]

The probe sets have been designed to be within the workable 3' amplified
region under normal circumstances. It maybe worth examining particularly
when you are working with small RNA samples and doing 2 rounds of
amplification.


-----Original Message-----
From: Zhang, Xueqing
To: bioconductor
Sent: 13/02/03 17:24
Subject: RE: [BioC] Quality of Affy Chips with the affy package

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

-----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.

	-oli-
-- 
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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