Hi, The Li and Wong method uses the .cel file generated by MAS. What I believed the bg.correct=MAS in order to exactly mimic it. I don't know why to use bg.correct=FALSE in your analysis. Thanks. L. 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 >

Actually I believe that it is a slightly modified version of the MAS background that is used in dChip. They use a 10 by 10 grid rather than 4 by 4. Ben On Wed, 2004-09-29 at 08:37, Lizhe Xu wrote: > Hi, > The Li and Wong method uses the .cel file generated by MAS. What I believed the bg.correct=MAS in order to exactly mimic it. > I don't know why to use bg.correct=FALSE in your analysis. > > Thanks. > > L. > > 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 > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad