[BioC] OT: van 't Veer (2002) classifier

[Francois Pepin]

Hi Gad,

I don't know of a reference implementation for this. The differences you 
explain depend on whether you want a more specific or a more sensitive 
classifier. As you mentioned, different variations have been used in the 
different papers about it.

Just decide what you want to do (maximizing accuracy is generally a 
decent choice) or choose one publications and you'll be fine.

Francois

Gad Abraham wrote:
> A non-BioC question:
> 
> Does anyone know of an authoritative implementation of the van 't Veer 
> et al (2002) breast cancer metastasis classifier?
> 
> There seem to be different interpretations in the literature, in some 
> places (e.g., van de Vijver 2002, Tibshirani & Efron 2002, Mansmann et 
> al2006) it's described as classifying each sample according to whether 
> the correlation with the centroid of good prognosis cases is above some 
> threshold, and in others the classification is the class with the 
> centroid that has highest correlation with the sample (which is how I 
> interpret van 't Veer 2002).
> 
> Thanks,
> Gad
>