[BioC] Cutoff to use for IQR filtering in genefilter

[Seungwoo Hwang]

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
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Seungwoo Hwang, Ph.D.
Senior Research Scientist
Korean Bioinformation Center