Hi Javier, Javier P?rez Florido wrote: > Thanks Jim, but, what is the method to be used in the background > correction? I have read that in this step (background) the MM > intensities are substracted. This is just a question of semantics. What you want is for the MBEI method to be fit on the PM-MM data - does it really matter if you say "I'm going to subtract MM from PM as a background correction." or if you say "I'm going to subtract MM from PM as a PM correction method."? In the end you have done the same thing. Best, Jim > Thanks again, > Javier > > > James W. MacDonald escribi?: >> Hi Javier, >> >> Javier P?rez Florido wrote: >>> Hi all, >>> >>> The MBEI method has two versions: PM-only and PM-MM. >>> PM-only model performs no background correction, Invariant Set for >>> normalization, PM only for PM correction and the Multiplicative Model >>> for summarization. Using expresso: >>> eset<-expresso(affyBatch,bgcorrect.method="none",normalize.method= "invariantset", >>> pmcorrect.method="pmonly",summary.method="liwong") >>> >>> But, what is the expresso command for the PM-MM model? >> >> pmcorrect.method = "subtractmm" >> >> > pmcorrect.methods() >> [1] "mas" "methods" "pmonly" "subtractmm" >> [5] "orrect.methods" >> >> >> Best, >> >> Jim >> >> >>> >>> Thanks in advance, >>> Javier >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826