[BioC] nsFilter cutoff

[James W. MacDonald]

Hi James,

james perkins wrote:
> Hi,
> 
> I am finding the nsFilter IQR cutoff somewhat confusing.
> 
> It says it is using IQR with a default cutoff of 0.5.
> 
> This gives the impression that if you line up the data and take the 
> value between the 0.25 and 0.75 quantiles, you would keep the probeset 
> if this value was < 0.5
> 
> However this is not the case, so I would like to know how exactly does 
> this work?

Actually it _is_ the case - perhaps you misunderstand something.

First, get all probesets with an IQR > 0.5
 > T1 <- apply(exprs(sample.ExpressionSet), 1, IQR) > 0.5

Now do the same using nsFilter()
 > T2 <- nsFilter(sample.ExpressionSet, FALSE, filterByQuantile = FALSE, 
feature.exclude="", remove.dupEntrez = FALSE)

Are they the same?
 > all.equal(featureNames(sample.ExpressionSet)[T1], featureNames(T2$eset))
[1] TRUE

Best,

Jim



> 
> Regards,
> 
> James
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623