Question: Cutoff to use for IQR filtering in genefilter

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Seungwoo Hwang •

**80**wrote:I am wondering what cutoff value I should use for IQR filtering in
genefilter. I did some literature search. It varies from paper to
paper. I have read two papers so far. One used 0.5, the other used
0.18. affylmGUI has an option of 0.5, 0.25, and 0.1.
I also searched Bioconductor archive and read that Dr. Robert
Gentleman suggested to filter out the genes whose IQR below median,
not for some fixed value.
I have two questions on this vein.
(1) How small is a gene's variance (in terms of number) if its IQR is
some value, say, 0.5 or 0.1? Can I calculate it?
(2) When median is used instead of fixed number, wouldn't it be too
large, since median of a gene's expression intensities across samples
can be anything?
Thanks,
Seungwoo
------------------------------------
Seungwoo Hwang, Ph.D.
Senior Research Scientist
Korean Bioinformation Center

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modified 11.5 years ago
by
Mark Cowley •

**400**• written 11.5 years ago by Seungwoo Hwang •**80**