[BioC] Limma:short question

[James Wettenhall]

Julia,

Yes, if using lm.series, you should give it log-transformed 
data.  If you create an exprSet object with rma it will be 
automatically log-transformed, and you can then pass the exprSet 
object directly into lmFit which will call lm.series.

Hope this helps,
James

 On Tue, 27 Jan 2004, Julia Engelmann wrote:

> Hi all,
> 
> I am using limma on Affymetrix data and want to fit a linear model with
> 
> fit <- lm.series(exprs(E), design)
> 
> My question is:
> Is the data in E supposed to be on a log scale (like after using vsn) or not?
> 
> Thanks for your help,
> Julia
> 
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