[BioC] log values of affybatch data

[Rafael A. Irizarry]

li wong returns original/antilog scale. originally, the idea was to return
values in the scale which the model, used for the data reduction,
suggests one should perform tests. so for li and wong's model (additive
error) it comes back as original scale. for the medianpolish function used
by rma (multiplicative error) it comes back in the log scale. because its
not clear what the model is for mas5 and mas4 (avdiff)  original scale is
returned for consistency with their software. i believe vsn returns values
in the scale they suggest one should perform test, i.e. with the variance
stabilizing transformation applied. hopefully this isnt too confusing.  i
believe/hope the help files say what scale is used. 




On Tue, 30 Sep 2003, Ann Hess wrote:

> 
> Does expresso ALWAYS return logged data?  For example, when calling the
> LiWong algorithm using
> 
> expresso(data,normalize.method="invariantset",bg.correct=FALSE,
> 	pmcorrect.method="pmonly",summary.method="liwong")
> 
> does that return expression values on the log or original scale?
> 
> 
> 
> On Tue, 30 Sep 2003, James MacDonald wrote:
> 
> > Assuming you want the log of the PM data, you would do log2(pm(abatch)).
> > For log2(MM), substitute mm for pm.
> >
> > Note also that expresso and rma return logged data, so you would not
> > want to input pre-logged data to these functions.
> >
> > Jim
> >
> >
> >
> > James W. MacDonald
> > Affymetrix and cDNA Microarray Core
> > University of Michigan Cancer Center
> > 1500 E. Medical Center Drive
> > 7410 CCGC
> > Ann Arbor MI 48109
> > 734-647-5623
> >
> > >>> Stephen Nyangoma <S.Nyangoma at cs.rug.nl> 09/30/03 12:50PM >>>
> > Hi all,
> > How can I compute the logs of the Affybatch data?
> >
> > Stephen.
> >
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