[BioC] log values of affybatch data

[Ann Hess]

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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