[BioC] normexp background correction

[Gordon Smyth]

>Date: Mon, 7 Nov 2005 22:14:25 +1100 (EST)
>Subject: [BioC] normexp background correction
>From: "Gordon K Smyth" smyth at wehi.edu.au
>To: "Edoardo Giacopuzzi" gedoard at bluebottle.com
>Cc: bioconductor at stat.math.ethz.ch
>
> > Date: Thu,  3 Nov 2005 03:59:35 -0600
> > From: Edoardo Giacopuzzi gedoardo at bluebottle.com
> > Subject: [BioC] normexp background correction
> > To: bioconductor at stat.math.ethz.ch
> >
> > I'm using limma package to perform microarray data analysis. I've
> > tried different backgorund correction methods, expecially normexp and
> > edwards. I've read that normexp is considered the best by now, but I
> > can't found any detailed information about it (how it works on data
> > and so on).
> > Does anyone know where I can get this kind of information?
> >
> > Thanks!
> > Edoardo (University of Brescia)
>
>I'm the author of the normexp method, but I haven't yet published a 
>detailed description.  Sorry.
>
>Gordon

It may help that normexp was used in the following two publications. The 
method was actually invented for use in the first publication, and the 
second publication is probably the best reference at this time.

Regards
Gordon

Peart, M. J., Smyth, G. K., van Laar, R. K., Richon, V. M., Holloway, A. 
J., Johnstone, R. W. (2005). Identification and functional significance of 
genes regulated by structurally diverse histone deacetylase 
inhibitors.  Proceedings of the National Academy of Sciences of the United 
States of America.102, 3697-3702.

Smyth, G. K. (2005). Limma: linear models for microarray data. 
In:  Bioinformatics and Computational Biology Solutions using R and 
Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber 
(eds.), Springer, New York, pages 397-420.