[BioC] Quality of Affy Chips with the affy package

[Rafael A. Irizarry]

the affy vignette gives a detailed explanation of what the AffyRNAdeg
function does. interpreting the graph and summary stats  is up those who
really understand the biology/chemistry. please share opinionns if you
have them.
-r
On Thu, 13 Feb 2003, Zhang, Xueqing wrote:

> 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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>