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

Ann Hess hess at stat.colostate.edu
Sat Sep 18 22:09:03 CEST 2004


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



More information about the Bioconductor mailing list