[BioC] question regarding genefilter package

[James W. MacDonald]

Hi Whomever,

zrl wrote:
> Dear list,
> I am bit confused about the meaning of "var.cutoff" in function of
> "nsFilter". Since we calculate the IQR of each gene, how could the
> var.cutoff is a absolute value, 0.5.
> When I read the help document, it says "Note that by default the
> numerical-filter cutoff is interpreted as a quantile..." Does it mean
> we really compare the IQR with region of quantile 0 to quantile 0.5?
> Could someone help me clarify this? Thanks.

I'm not sure what you are asking, so I'll just take a stab at it.

The 'stock' setting of nsFilter takes each row of the data in your 
ExpressionSet and computes the IQR for that row. It then calculates what 
the median IQR is, and then removes the 50% of the data that have an IQR 
below that value.

So if you change the var.cutoff to 0.2, you would remove the data with 
an IQR below the first quintile. Or if you changed var.cutoff to 0.75, 
you would remove the data with an IQR below the third quartile.

Best,

Jim


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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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