[BioC] RNA degradation problem

[Naomi Altman]

It looks to me as if there is a problem in this experiment.  I cannot 
speak for the efficacy of the RNA degradation plot.  But unless a 
large amount of differential expression occurs in this experiment, 
the very close similarity between the duplicates compared to the 
other conditions leads me to thing that these duplicates were either 
not biological replicates, or the duplicates were processed together 
causing correlation.

I have seen this type of thing with spotted arrays when arrays 
processed in a single batch are much more similar than biological 
replicates processed on different days.

--Naomi

At 08:12 AM 1/18/2006, James W. MacDonald wrote:
>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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> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
>--
>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
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111