[BioC] ad hoc (was :question abour background subtraction in RMA)

[Stefano Calza]

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 at 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 
> Nestlé Research Center 
> PO Box 44, CH-1000 Lausanne 26 
> Phone: + 41 21 785 9433 
> <mailto:nicolas.antille at rdls.nestle.com>
> 
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-- 
Stefano Calza,
Sezione di Statistica Medica
Dip. di Scienze Biomediche e Biotecnologie
Università degli Studi di Brescia - Italy
Viale Europa, 11 25123 Brescia
email: calza at med.unibs.it
Telefono/Phone: +390303717532
Fax: +390303701157