[BioC] VSN package: vsnrma generate different values from the same data

[Wolfgang Huber]

Dear Xiaokuan

slight differences can be expected due to the probe sampling that is 
used in the vsn2 method for AffyBatch to increase the speed of the 
computation. You can switch off the sampling e.g. by specifying 
"subsample=0" in the call to vsnrma. And you can make the sampling 
deterministic by calling set.seed before vsnrma.

However, such differences should always be small compared to the 
precision of the data themselves - i.e., they should be negligible. If 
they are not, something is foul. I would be interested in a reproducible 
example: sessionInfo(), exact script used, the necessary data objects.

  Best wishes
	Wolfgang



On Jun/30/10 9:26 PM, Xiaokuan Wei wrote:
> Dear List,
>
> I have applied "vsnrma" commpand to an affybatch object. But for the same object, if I run multiple times vsnrma, it gives me different values.
> i.e.
>
> dat1<-vsnrma(obj)
> dat2<-vsnrma(obj)
> dat3<-vsnrma(obj)
>
>
> dat1,dat2,and dat3 are different. It's not just numerically marginally different, but rather larget different.
> for example, probe A, for dat1, the value is 3, dat2 is 4, dat3 is 5.
>
> Could Wolfgang or someone explain this to me? Is there a way to seed a value and make the results same?
>
> Thank you.
>
> Xiaokuan
>
>
>
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>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber