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
Hi Ruppret,
check the vsn package, its vignette and the references therein. The
function vsn estimates the parameters of a model that is derived from
the multiplicative-additive error model, in particular, parameters of
the glog transformation.
Cheers
Wolfgang
Ruppert Valentino wrote:
> 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
>
-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax: +44 1223 494486
Http: www.ebi.ac.uk/huber
The closest thing to the two component error model you're referring
to (I think) is the Rocke, Durbin model (Bioinformatics, 2003, 19,
966-972). The last time I checked, there was code on David Rocke's
web site. I think I've seen an R package there as well. Otherwise,
still within the microarray framework, there's the VSN package, which
performs essentially the same job (variance stabilization). I'd
suggest reading any vignettes or user manuals available for the
packages to get a handle on using the code. You may also want to look
at the original papers.
Cheers,
--------------------------------------------
Greg Finak
PhD Candidate
McGill Center For Bioinformatics
W: (514)398-7071 x09317
emai: finak at mcb.mcgill.ca
--------------------------------------------
On 6-Dec-05, at 6:54 PM, Ruppert Valentino wrote:
> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
