[BioC] Limma:short question

[Wolfgang Huber]

References:<200401271715.30817.julia.engelmann at biozentrum.uni-wuerzburg.de>

Hi Julia,

Julia Engelmann wrote:
> 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?

Generally yes. The engine behind lm.series is lm.fit, a linear least
squares regression that assumes that the data is at least approximately
identically and normally distributed. That assumption is more likely
to hold with data transformed by vsn (or otherwise reasonably
background-corrected and log-transformed) than with data on the original
scale.

The estimated effects from the linear model will then be intepretable as
"average fold changes".

Best wishes
   Wolfgang

-- 
-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/abt0840/whuber