On Fri, Jun 13, 2003 at 09:18:26AM -0400, James MacDonald wrote: > Ad hoc is a latin term that literally means 'for this'. It means that > something is done either temporarily or only for a specific use. In this > case, I believe that it means the background estimation was temporary, > and would be improved in the future. Actually ad hoc means "for this (purpose )". So it means that a function was made specifically for that task, on purpose. Stefano > You can get an idea of how the parameters are estimated by viewing the > code for the functions bg.correct.rma, bg.adjust, and bg.parameters. The > actual code for RMA is written in C, so if you want to know exactly how > they are estimated you will have to look at that. > > In addition, I believe Ben Bolstad has some manuscripts on his website > that have more details about the RMA background. Just google his name > and you can find it. > > HTH, > > Jim > > > > James W. MacDonald > UMCCC Microarray Core Facility > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > >>> "Antille,Nicolas,LAUSANNE,NRC-BAS" > <nicolas.antille@rdls.nestle.com> 06/13/03 07:34AM >>> > Hello! > > I'm currently studying in details the Robust Multichip Average > procedure for > normalizing microarrays data. I am particulary intersted in the > background > subtraction. In the description of the affy package, it is said the > the > function bg.parameters provides adhoc estimates of the parameters of > the > normal and exponential distributions. What does the word adhoc means? > Can someone explain me the way these parameters are estimated? > > Thanks in advance! > > Regards > > Nicolas > > > Nicolas Antille > Statistician > Nestl? Research Center > PO Box 44, CH-1000 Lausanne 26 > Phone: + 41 21 785 9433 > <mailto:nicolas.antille@rdls.nestle.com> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Stefano Calza, Sezione di Statistica Medica Dip. di Scienze Biomediche e Biotecnologie Universit? degli Studi di Brescia - Italy Viale Europa, 11 25123 Brescia email: calza@med.unibs.it Telefono/Phone: +390303717532 Fax: +390303701157