[BioC] dChip

[Ben Bolstad]

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
> > 
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> >
> 
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-- 
Ben Bolstad <bolstad at stat.berkeley.edu>
http://www.stat.berkeley.edu/~bolstad