[BioC] RNA degradation problem

[James W. MacDonald]

fhong at salk.edu wrote:
> Dear list,
> 
> I have this 8 affy arrays under 2*2 factorial design, with duplicates
> under each condition. The RNA degradation plot worries me since the slopes
> from 8 arrays are so different, with duplicates under each condition as
> one group (see the QC plots at http://cactus.salk.edu/temp/QC-1.jpeg)
> I would suspect that these arrays were processed  under different levels
> if amplification.
> 
> My problem is how to handle this data set beside doing the normalization?
> Will this pattern seriously bias the result? I read some previous message
> about this topic, just hope to get more information.

I find that the RNA degradation plots are less useful for indicating 
possible problems than the density plots. If the density plots are all 
reasonably similar, in my experience the normalization should be fine. 
Another excellent plot for detecting problems is the residual plot in 
the affyPLM package.


Best,

Jim


>
> Many thanks!
> Fangxin
> 
> 
> --------------------
> Fangxin Hong  Ph.D.
> Plant Biology Laboratory
> The Salk Institute
> 10010 N. Torrey Pines Rd.
> La Jolla, CA 92037
> E-mail: fhong at salk.edu
> (Phone): 858-453-4100 ext 1105
> 
> 
> 
> --------------------
> Fangxin Hong  Ph.D.
> Plant Biology Laboratory
> The Salk Institute
> 10010 N. Torrey Pines Rd.
> La Jolla, CA 92037
> E-mail: fhong at salk.edu
> (Phone): 858-453-4100 ext 1105
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623