Entering edit mode
Lizhe Xu
▴
210
@lizhe-xu-666
Last seen 10.3 years ago
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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