I was wondering if there was a way to obtain background (or non- specific binding) corrected values for the Li Wong PMonly method. Li and Wong state their model as PM_ij = v_j + Theta_i*phi_j + e. Is it possible to find the value PM_ij - v_j? Is the command: expresso(affybatch.example,normalize.method="invariantset", bg.correct=FALSE,pmcorrect.method="pmonly",summary.method="liwong") making this "background correction"? The background term cancels for the PM-MM model, but not for the PM only model. Thanks Ann

Ann, A more exact way to mimic the Li and Wong method with the command expresso is: expresso(affybatch, normalize.method="invariantset", bg.correct=FALSE, pmcorrect.method="subtractmm", summary.method="liwong") As you say, Li and Wong state their model as: PM_ij - v_j = Theta_i*phi_j + e with v_j a background term. (One can note that is currently disputed whether MM_ij is an appropriate background term or not.) remark: If you use this often you can make your own wrapper liandwong <- function(abatch, ...) { expresso(affybatch, normalize.method="invariantset", bg.correct=FALSE, pmcorrect.method="subtractmm", summary.method="liwong", ...) } Hoping this helps, L. Ann Hess wrote: > I was wondering if there was a way to obtain background (or non- specific > binding) corrected values for the Li Wong PMonly method. Li and Wong > state their model as PM_ij = v_j + Theta_i*phi_j + e. Is it possible to > find the value PM_ij - v_j? > > Is the command: > expresso(affybatch.example,normalize.method="invariantset", > bg.correct=FALSE,pmcorrect.method="pmonly",summary.method="liwong") > making this "background correction"? > The background term cancels for the PM-MM model, but not for the PM only > model. > > Thanks > > Ann > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >