[BioC] dChip, liwong, probe response or phi

[lgautier at altern.org]

You can probably hack it quickly by
1- running the preprocessing steps 'background correction',
'normalization' and 'PM correction' on your 'AffyBatch'
2- then running an edited version of the method 
'generateExprset.methods.liwong' (returning 'phi' as an attribute for
example - see help(attr)).


L.


> Hi,
> I've looked through the archives to see if this question had been
> raised before, and not finding anything about it, thought I'd ask.
>
> I'm wondering if there is a way to get the phi values returned as
> output when running expresso with the liwong method settings. Phi
> values in the dChip model are the "probe sensitivity index" (PSI).
>
> I know that expresso just returns the summarized expression value for a
> probeset (gene) which is the Theta in the dChip model below:
>
> PM_ij - v_j = Theta_i*phi_j + e
> with v_j a background term.
>
> If not expresso, are there other functions or methods that can be
> tweaked to return the PSI values along with the Theta? If anyone has
> tried this before, I'd appreciate your insights.
>
> Thanks,
> Hemali
>
> Hemali Patel
> Department of Biomedical Engineering
> Boston University
>
>
> 	[[alternative text/enriched version deleted]]
>
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