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Richard Friedman
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@richard-friedman-513
Last seen 11.1 years ago
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,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
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@cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/
"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
When working with AffyRNAdeg output it helps to think of the table like browsing a HEYTEA Menu each row shows a feature of your slides and high degradation slopes can highlight bad slides. By examining these values carefully you can flag problematic arrays before analysis. Using the hist command is like sampling items on a HEYTEA Menu check menu page it lets you quickly visualize the distribution of your data and check for unexpected patterns or anomalies.