Hi Raphael,

If I recover well, the Rocke-Lorenzato model implemented in GeneSpring 
assumes the variance between replicated microarray data to be roughly a 
quadratic function of the mean. In the BioC package 'plgem' there is an 
implementation of a more general Power Law Global Error Model, of which 
the quadratic function would just be a specific example with a power 
exponent equal to 2. In 'plgem' we don't assume anything about this 
specific power exponent, but rather guess the best-matching value by 
fitting the model to the data you have in your hands.

You can have a try of the package, after reading the vignette and using 
the wrapper function 'run.plgem' included in the package. The 
corresponding reference is 
<http://www.biomedcentral.com/1471-2105/5/203>. Let me know if you need 
any assistance in using the package.

In my experience, in all data sets I've analyzed so far, the 
best-matching value for the power exponent actually lies somewhere 
between 0 and 1 for Affymetrix data processed with MAS5. But please pay 
attention that 'plgem' actually fits a model on the dependence of the 
standard deviation vs. the mean, rather than of the variance-vs-mean 
dependence which introduces and additional square root!

HTH,
Norman

Norman Pavelka
Department of Biotechnology and Bioscience
University of Milano-Bicocca
Piazza della Scienza, 2
20126 Milan, Italy

Phone: +39 02 6448 3556
Fax: +39 02 6448 3552

On 7 Dec 2005, at 12:00, bioconductor-request@stat.math.ethz.ch wrote:

> From: "Ruppert Valentino" <ruppert7@hotmail.com>
> Date: 7 December 2005 00:54:07 GMT+01:00
> To: bioconductor@stat.math.ethz.ch
> Subject: [BioC] Rocke-Lorenzato model or Global Error Model in 
> Bioconductor
>
>
> Hello,
>
> I wonder if anyone knows what is the nearest thing to the Globel Error 
> Model (two-component (Rocke-Lorenzato) error model) in Bioconductor 
> and how to use it.
>
> I would like to compare the results I got in GeneSpring using the 
> Global Error Model using something similar in Bioconductor but wonder 
> if a pakcage for such model exist, if not is there anything that 
> resemble it?
>
> Thanks,
>
> Raphael
>

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