[BioC] PDNN for affy.

Laurent Gautier laurent at cbs.dtu.dk
Mon Oct 13 10:36:03 MEST 2003

Hi Stephen,

Note that the pack 'affypdnn' was developped under R-1.7.1,
but it should work out-of-the-box with R-1.8.0 and/or
the latest devel version of 'affy'.

I shall see if we can cram a short moment to include a function
to do that before the end of the week...


On Mon, Oct 13, 2003 at 10:01:55AM +0200, Stephen Nyangoma wrote:
> 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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Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent

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