[BioC] question regarding genefilter package

[zrl]

Thank you Jim. I think you pretty much answered my questions. So, the
"var.cutoff" is actually the quantile of the IQRs calculated of all
the rows/genes. Do I understand this right?

Thanks.

Qiudao.

On Tue, Feb 2, 2010 at 2:28 PM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
> 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
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