[BioC] Re: RNA degradation

[Leslie M. Cope]

On Tue, 22 Jul 2003 bioconductor-r
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> Today's Topics:
> 
>    1. implementation of an add-on package (Stephen Moore)
>    2. RNA degradation plot (Bill Kenworthy)
>    3. R Hangs (michael watson (IAH-C))
>    4. Affy digestion plots (Oliver Hartmann)
> 
> 
> ----------------------------------------------------------------------
> Using the affy library, I did an RNA degradation plot for 5 mu74Av2
> mouse chips and it generated the figures below.  I do not have anything
> to measure this against - if someone has some figures on what "degraded"
> RNA looks like (and/or some thresholds), and a representative plot I
> would be appreciative.
> 
> slope -0.0201 -0.236 -0.228 -0.0884 -0.209
> pvalue 0.858 0.0517 0.0751 0.44 0.115
> 
> Thanks
> BillK

I used mainly HGU95a chips in developing the method.  for that chiptype, 
232 very high quality chips had slopes between .05 and .3  Comparison of 
other hgu95a chips to 
the 3'/5' housekeeping ratios suggest that slopes close to 1 (.75 to 1.05)  
are 
borderline, whereas slopes larger than 1.1 seem to indicate very bad 
quality rna. slope does not appear to be a linear measure of RNA quality.  
 This is based on small sample though and does 
not yet 
consititute a rule. We hope to have large sample validation coming soon.
 I 
would say that your mouse chips here look great.

The one large hgu133 experiment I looked at had slopes much higher than 1, 
although 
3'/5' ratios were all good.  I don't know what to say about that chipset 
yet.  chips a and b were similar though.

Leslie Cope

> -------------------------