[BioC] Li Wong PM-only "background" correction

[Laurent Gautier]

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
> 
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