[BioC] PDNN for affy.

Stephen Nyangoma S.Nyangoma at cs.rug.nl
Mon Oct 13 10:01:55 MEST 2003

Hi all,
I am implementing the R for PDNN model by Laurent in R-1.7.1. The
function find.params.pdnn works ok and I can obtain the Bs, Ns, Fs and
the lambdas. I want to use equation 1 in the paper

Li Zhang, Michael F. Miles and Kenneth D. Aldape -
A model of molecular interactions on short oligonucleotide
arrays, 2003, Nature Biotech., vol. 21, n.7

to obtain the fitted values. At the moment, I cannot see how to obtain
the Es (especially the E^*, the average free energy for NSB). Does
anyone have an idea of how to generate these values?

Regards. Stephen.

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