[BioC] nsFilter cutoff

[james perkins]

Hi James

I meant when we have filterByQuantile as TRUE. In this case it seems to 
behave differently, and I can't figure out why, and I don't want to guess!

Regards,

Jim

James W. MacDonald wrote:
> 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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>