[BioC] Interpretation of output of AffyRNAdeg and hist commands

James MacDonald jmacdon at med.umich.edu
Fri May 7 15:27:45 CEST 2004

The table simply gives you the slope from a linear regression of the 3'
- 5' ordered means, as well as a p-value from a test of the null
hypothesis that the slope = 0. See ?AffyRNAdeg for a more in-depth

In my experience, the plot (plotAffyRNAdeg) is good for finding 'bad'
chips; I simply look for chips that have a significantly different slope
than the rest of the chips. By significant, I mean that
'eyeballometrically' it seems quite different.

The density plot (resulting from a call to hist()) is also good for
finding outlier chips. We have been having a bad run recently with
high-background chips, and these always have a distribution that is much
less right-skewed than the other chips, and is also shifted
significantly to the right. Again, this is eyeballometric analysis.

Any chip that has a significantly different shape and/or location than
the other chips in a batch invariably shows up as an outlier (as
determined by the residual plots you can do with affyPLM, and PCA on the
expression values), so I routinely re-do chips that look bad on the
density plot. Note here that location seems to be much more important
than shape.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> Richard Friedman <friedman at cancercenter.columbia.edu> 05/06/04
03:54PM >>>
Dear Bioconductor Users,

	I am not clear on the meaning of the table that is output
from the AffyRNAdeg and how to use it to find bad slides.
I am also not clear on how to use the hist command to
see if the data is as it should be. I would appreciate any
pointers or literature references.

Thanks and best wishes,
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu 

"I'm giving up coffee. Now that it looks like I might top
6 feet, I don't want to risk spoiling it."
- Isaac Friedman, age 14

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