I would like to understand where do affinity.spline.coefs used in function compute.affinities come from ? 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| tél: (33) (0)1.44.08.16.73 http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/ fax: (33) (0)1.44.08.16.66 [[alternative HTML version deleted]]

On Thu, 18 Nov 2004, aubert@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| > tél: (33) (0)1.44.08.16.73 > http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/ > fax: (33) (0)1.44.08.16.66 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >