Question: Rocke-Lorenzato model or Global Error Model in Bioconductor
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gravatar for Ruppert Valentino
13.6 years ago by
Ruppert Valentino270 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
genespring • 427 views
ADD COMMENTlink modified 13.6 years ago by Norman Pavelka190 • written 13.6 years ago by Ruppert Valentino270
Answer: Rocke-Lorenzato model or Global Error Model in Bioconductor
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gravatar for Wolfgang Huber
13.6 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
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
ADD COMMENTlink written 13.6 years ago by Wolfgang Huber13k
Answer: Rocke-Lorenzato model or Global Error Model in Bioconductor
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gravatar for Greg Finak
13.6 years ago by
Greg Finak50
Greg Finak50 wrote:
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
ADD COMMENTlink written 13.6 years ago by Greg Finak50
Answer: Rocke-Lorenzato model or Global Error Model in Bioconductor
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gravatar for Norman Pavelka
13.6 years ago by
Norman Pavelka190 wrote:
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ADD COMMENTlink written 13.6 years ago by Norman Pavelka190
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