[BioC] AffyRNAdeg slopes

[James MacDonald]

Like expression values, I don't think there is a 'good' value for the
slope. Of more concern is how the slopes compare within a given set of
chips. If they are all relatively parallel, this indicates that the RNA
degradation and/or in vitro transcription were relatively similar for
all of the samples. Since you are only interested in comparisons within
a given set of chips, this is much more critical than an absolute
slope.

Anyway, in my experience, large differences in slope are less critical
than big differences between the density plots. I find that outliers on
the density plot nearly always require a redo of the chip, whereas chips
with very different slopes in the RNA degradation plot may be usable.

HTH,

Jim



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

>>> David Carter <dcarter at robarts.ca> 06/08/04 01:45PM >>>
Hello everyone,
I was wondering what are acceptable values for the slopes generated 
using summaryAffyRNAdeg in the affy package.  I assume 0.0 would be the

ideal, but what values would be considered 'of concern', or too high? 

Any thoughts from users of the RNA deg function?
Thanks.

-- 
David Carter
London Regional Genomics Centre
Robarts Research Institute, Room 4.01
PO Box 5015, 100 Perth Drive
London, Ontario, Canada, N6A 5K8

phone:	(519) 663-3253
fax:	(519) 663-3037

dcarter at robarts.ca 
http://www.lrgc.ca/ 

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