Rocke-Lorenzato model or Global Error Model in Bioconductor
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@ruppert-valentino-1376
Last seen 9.6 years ago
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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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
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
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Greg Finak ▴ 50
@greg-finak-1495
Last seen 9.6 years ago
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
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@norman-pavelka-1214
Last seen 9.6 years ago
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