[BioC] gcrma package

[Zhijin Wu]

On Thu, 18 Nov 2004, aubert at inapg.fr wrote:

> I would like to understand where do affinity.spline.coefs used in function 
> compute.affinities come from ?

These were estimated from an array having non-specific binding only.

The reference can be downloaded here
http://www.bepress.com/jhubiostat/paper1/ 

Wu, Z, Irizarry, RA, Gentleman,
R, Martinez Murillo, F, Spencer, F (2004) A Model Based Background
Adjustement for Oligonucleotide Expression Arrays. (To appear in JASA.)

> 
> library(gcrma)
> data(affinity.spline.coefs)
> 
> affinity.spline.coefs
> X1 X2 X3 X4 X5 X1
> -0.55004171 -0.58579091 -0.08870557 -0.47774242 0.23205570 0.58002746
> X2 X3 X4 X5 X1 X2
> 0.61274425 0.10294309 0.57388808 -0.28334367 0.01350914 -0.02030805
> X3 X4 X5
> -0.14747469 0.05436463 -0.10124882
> 
> I read the reference
> Hekstra, D., Taussig, A. R., Magnasco, M., and Naef, F. (2003)
> Absolute mRNA concentrations from sequence-specific calibration of
> oligonucleotide array. Nucleic Acids Research, 31. 1962-1968,
> but don't find any answer to my question.
> 
> 
> Thank you in advance!
> 
> Julie AUBERT
> 
> 
> Julie AUBERT
> Unité Mixte de Recherche INA-PG (dépt OMIP) / INRA (dépt Mathématiques et 
> Informatiques Appliquées)
> 16 rue Claude Bernard F-75231 Paris cedex 05 FRANCE|
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> 
> 
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